Telomerase activity assays

ABSTRACT

Telomerase activity in a sample can be measured using a two reaction protocol. The first reaction involves the formation of telomerase substrate extension products from a telomerase substrate. The second reaction involves replication of the telomerase substrate extension products and/or amplification of signal generated by a bound probe. The presence of telomerase activity in a human somatic tissue or cell sample is positively correlated with the presence of cancer and can be used to diagnose a disease or other conditions of medical interest, as well as the course of disease progression or remission in a patient.

The invention described herein was made with Government support under agrant from the Department of Health and Human Services. The Governmenthas certain rights in this invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation-in-part of U.S. patentapplication Ser. No. 08/482,132, filed Jun. 7, 1995, which is acontinuation-in-part of Ser. No. 08/315,214, filed 28 Sep. 1994, nowU.S. Pat. No. 5,629,154, which is a continuation-in-part of Ser. No.08/255,774, filed 7 Jun. 1994, which is a continuation-in-part of Ser.Nos. 08/151,477 and 08/153,051, now U.S. Pat. No. 5,645,986, both ofwhich were filed 12 Nov. 1993. Each of the foregoing patents and patentapplications is incorporated herein by reference.

INTRODUCTION

1. Technical Field

The present invention relates to telomerase, a ribonucleoprotein enzymeinvolved in telomere DNA synthesis, and provides assays and materialsfor identifying and measuring telomerase activity. The invention relatesto the fields of molecular biology, chemistry, pharmacology, and medicaldiagnostic and prognostic technology.

2. Background

Telomeres are specialized structures at the ends of eukaryoticchromosomes that function in chromosome stabilization, positioning, andreplication (Blackburn and Szostak, 1984, Ann. Rev. Biochem. 53:163-194;Zakian, 1989, Ann. Rev. Genetics 23:579-604; Blackburn, 1991 Nature350:569-573). In all vertebrates, telomeres consist of hundreds tothousands of tandem repeats of 5'-TTAGGG-3' sequence and associatedproteins (Blackburn, 1991; Moyzis et al., 1988, Proc. Natl. Acad. Sci.85:6622-6626). Southern blot analysis of chromosome terminal restrictionfragments (TRF) provides the composite lengths of all telomeres in acell population (Harley et al., 1990, Nature 345:458-460; Allsopp etal., 1992, Proc. Natl. Acad. Sci. USA 89:10114-10118; Vaziri et al.,1993, Am. J. Human Genetics 52:661-667). In all normal somatic cellsexamined to date, TRF analysis has shown that the chromosomes lose about50-200 nucleotides of telomeric sequence per cell division, consistentwith the inability of DNA polymerase to replicate linear DNA to the ends(Harley et al., 1990; Allsopp et al., 1992; Vaziri et al., 1993; Watson,1972, Nature New Biology 239:197-201).

This shortening of telomeres has been proposed to be the mitotic clockby which cells count their divisions (Harley, 1991, Mut. Res.256:271-282), and a sufficiently short telomere(s) may be the signal forreplicative senescence in normal cells (Allsopp et al., 1992; Vaziri etal., 1993; Hastie et al., 1990, Nature 346:866-868; Lindsey et al.,1991, Mut. Res. 256:45-8; Wright and Shay, 1992, Trends Genetics8:193-197). In contrast, the vast majority of immortal cells examined todate shows no net loss of telomere length or sequence with celldivisions, suggesting that maintenance of telomeres is required forcells to escape from replicative senescence and proliferate indefinitely(Counter et al., 1992, EMBO 11:1921-1929; Counter et al., 1994, Proc.Natl. Acad. Sci. USA 91:2900-2940).

Telomerase, a unique ribonucleoprotein DNA polymerase, is the onlyenzyme known to synthesize telomeric DNA at chromosomal ends using as atemplate a sequence contained within the RNA component of the enzyme(Greider and Blackburn, 1985, Cell 43:405-413; Greider and Blackburn,1989, Nature 337:331-337; Yu et al., 1990, Nature 344:126-132;Blackburn, 1992, Ann. Rev. Biochem. 61:113-129). With regard to humancells and tissues, telomerase activity has been identified in immortalcell lines and in ovarian carcinoma but has not been detected atbiologically significant levels (that required to maintain telomerelength over many cell divisions) in mortal cell strains or in normalnon-germline tissues (Counter et al., 1992; Counter et al, 1994; Morin,1989, Cell 59:521-529). Together with TRP analysis, these resultssuggest telomerase activity is directly involved in telomeremaintenance, lining this enzyme to cell immortality.

Methods for detecting telomerase activity, as well as for identifyingcompounds that regulate or affect telomerase activity, together withmethods for therapy or diagnosis of cellular senescence andimmortalization by controlling or measuring telomere length andtelomerase activity, have also been described. See PCT patentpublication No. 93/23572, published Nov. 25, 1993, and 95/13382,published May 18, 1995, incorporated herein by reference. Theidentification of compounds affecting telomerase activity providesimportant benefits to efforts at treating human disease. Compounds thatinhibit telomerase activity can be used to treat cancer, as cancer cellsexpress and require telomerase activity for immortality, and most normalhuman somatic cells do not express telomerase activity. Compounds thatstimulate or activate telomerase activity can be used to treatage-related diseases and other conditions relating to cell senescence.

Known methods for assaying telomerase activity in cell samples rely onthe incorporation of radioactively labelled nucleotides into atelomerase substrate (Morin, 1989). The conventional assay uses anoligonucleotide substrate, a radioactive deoxyribonucleotidetriphosphate (dNTP) for labelling, and gel electrophoresis forresolution and display of products. Because telomerase stalls and canrelease the DNA after adding the first G in the 5'-TTAGGG-3' telomericrepeat, the characteristic pattern of products on the gel is a sixnucleotide ladder of extended oligonucleotide substrates. The phase ofthe repeats depends on the 3'-end sequence of the substrate; telomeraserecognizes where the end is in the repeat and synthesizes accordingly toyield contiguous repeat sequences. Although telomeric sequenceoligonucleotides are efficient in vitro substrates, telomerase will alsosynthesize repeats using substrates comprising non-telomeric DNAsequences.

Using such methods, scientists found that reliable telomerase extractionby hypotonic swelling and physical disruption of cells requires at least10⁷ -10⁸ cells and that the extraction efficiency varies between celltypes (Counter et al., 1992; Morin, 1989). There remains a need fortelomerase activity assays with increased sensitivity, speed, andefficiency of detecting telomerase activity as compared to theconventional assay, and this invention meets that need.

SUMMARY OF THE INVENTION

It is an object of the invention to provide a readily reproducible assaysystem for detecting telomerase activity, which is simple enough to usein the smaller (or low budget) clinical setting, but has the potentialfor high throughput using readily available robotics technology. Theassays can be used as diagnostic or prognostic aids, or for theidentification, screening, and development of molecules that act astelomerase inhibitors. The present invention also provides reagents,kits, and related methods and materials useful in the practice of theinvention.

In one aspect of the invention, a method is provided which comprises thesteps of:

(a) incubating a cell sample or an extract derived therefrom in areaction mixture comprising a telomerase substrate under conditions suchthat telomerase can catalyze extension of said telomerase substrate byaddition of telomeric repeat sequences;

(b) replicating the extended telomerase substrate; and

(c) correlating presence of telomerase activity in the cell sample withpresence of the extended telomerase substrate and absence of telomeraseactivity in the cell sample with absence of the extended telomerasesubstrate.

In one embodiment, the method involves the extraction of telomeraseactivity, if any, from a cell sample using, for example, a buffer thatcomprises a non-ionic and/or a zwitterionic detergent. The extractedtelomerase is used to mediate extension of a telomerase substrate in atelomerase substrate extension reaction. Alternatively, the telomeraseactivity is detected in situ, where a telomerase substrate isinternalized by the cells in a sample and then extended by thetelomerase in situ.

The extended telomerase substrate can be detected by numerous methods.In one embodiment, the extended telomerase substrate is replicated priorto detection by specific hybridization and subsequent extension of anoligonucleotide "primer" complementary to a telomeric repeat sequence. Anumber of useful reagents of the invention relate to this step.Typically, primer extension is mediated using a template-dependent DNApolymerase or ligase, and the primer is extended by addition ofnucleotides to the primer by the DNA polymerase.

The DNA polymerase used in this step is preferably a thermostable DNApolymerase. Using such a polymerase, one can conduct multiple cycles ofprimer extension, each cycle comprising the steps of (1) heating thereaction mixture to denature duplex DNA molecules; and (2) cooling thereaction mixture to a temperature at which complementary nucleic acidscan hybridize and the polymerase can extend the primer, withoutinactivating the polymerase. In this embodiment of the method, one canalso take advantage of the powerful Polymerase Chain Reaction ("PCR")technology by having an excess amount of the telomerase substrate, whichserves as one of the two primers for the PCR, in the reaction mixtureand performing the heating and cooling steps 5, 10, 15, 20, 30, or moretimes. In the PCR embodiment, the telomerase substrate lacks telomericrepeats to minimize primer dimer formation.

Alternatively, the primer extension can be mediated by atemplate-dependent DNA ligase, so that the primer is extended byaddition of an oligodeoxyribonucleotide to the primer by the DNA ligase.Typically, the DNA ligase is a thermostable DNA ligase, and the primerextension step is conducted by (1) heating the reaction mixture todenature duplex DNA molecules; and (2) cooling the reaction mixture to atemperature at which complementary nucleic acids can hybridize and theligase can extend the primer by ligation. In this embodiment of themethod, one can also take advantage of the powerful Ligase ChainReaction ("LCR") technology by having oligonucleotides ("ligomers")complementary to the extended primer in the reaction mixture and byperforming the heating and cooling steps from 5, 10, 15, 20, 30, or moretimes.

The present invention also provides a number of reagents such asoligonucleotides, primers, and oligomers, useful in the practice of thepresent invention. For instance, when one is using PCR to amplify anucleic acid, one needs to avoid nonspecific product formation. Suchproducts can form by a variety of methods, including via interaction ofthe primers used in the process to form "primer-dimers." The presentinvention provides primers and reaction conditions designed specificallyto minimize the problem of primer-dimer formation. In another aspect,the invention provides primers that limit the size of the largest primerextension product to no more than a defined number of telomeric repeatsmore than the largest products of telomerase-mediated extension of thetelomerase substrate. Control nucleic acids that can be used in aquantitative telomerase assay are also provided.

In a further embodiment, the method detects extended telomerase productsby employing RNA polymerase to synthesize multiple RNA copies of theproducts. In this case, the telomerase extended products contain apromoter sequence that is recognized by the RNA polymerase. Thus, amethod is provided which comprises the steps of:

(a) incubating a cell sample or an extract derived therefrom in areaction mixture comprising a telomerase substrate and a buffer in whichtelomerase can catalyze extension of the telomerase substrate byaddition of telomeric repeat sequences;

(b) adding to the reaction mixture a template-dependent RNA polymerasethat recognizes a promoter sequence operably linked to the telomerasesubstrate under conditions such that the RNA polymerase will form an RNAcopy of the extended telomerase substrate if an extended telomerasesubstrate is present in the reaction mixture; and

(c) correlating presence of telomerase activity in the cell sample withpresence of RNA copies of the extended telomerase substrate and absenceof telomerase activity in the cell sample with absence of the RNAcopies.

In one embodiment, RNA copies of the extended telomerase substrate canbe replicated by using reverse transcriptase to make DNA copies of theRNA.

In yet a further aspect of the invention, a method is provided thatcomprises the steps of:

(a) incubating a cell sample or an extract derived therefrom in areaction mixture comprising a telomerase substrate and a buffer in whichtelomerase can catalyze extension of the telomerase substrate byaddition of telomeric repeat sequences;

(b) immobilizing the telomerase substrate;

(c) adding to the reaction mixture a probe comprising a sequencesufficiently complementary to the extended telomerase substrate tohybridize specifically thereto under conditions such that if an extendedtelomerase substrate is present in the reaction mixture, the probe willhybridize to the extended telomerase substrate; and

(d) correlating presence of telomerase activity in the cell sample withpresence of the probe hybridized to extended telomerase substrate andabsence of telomerase activity in the cell sample with absence ofhybridization of the probe.

In a preferred embodiment, signal amplification is achieved by using abranched DNA probe. Such branched DNA probes can be used with or withouttarget nucleic acid amplification.

Irrespective of the replication method, the various reagents can belabelled to facilitate identification and quantitation oftelomerase-extended telomerase substrate.

The present invention also provides novel configurations of the reagentsuseful in the telomerase activity assay and kits comprising thosereagents to facilitate practice of the method. A kit comprises atelomerase substrate with or without instructions. A preferred kitcomprises the following reagents: CHAPS lysis buffer (10 mM Tris-Cl, pH7.5; 1 mM MgCl₂ ; 1 mM EGTA; 0.1 mM benzamidine (AEBSF, PMSF or similarreagents can be used in place of or in addition to benzamidine); 5 mMβ-mercaptoethanol; 0.5% CHAPS; 10% glycerol), 10×TRAP reaction buffer(200 mM Tris-Cl, pH 8.3; 15 mM MgCl₂ ; 630 mM KCl; 0.05% Tween 20; 10 mMEGTA; 1 mg/ml BSA), 50×dNTP mix (2.5 mM dATP, 2.5 mM dGTP, 2.5 mM dCTP,and 2.5 mM dTTP), TS primer (0.25 μl), water (PCR grade; protease, DNaseand RNase-free), positive control cell pellet (10⁶ cells) or a panel ofmultiple cell types with varying amounts of telomerase activity, a TRAPprimer mix (e.g., ACX 0.1 μg/μl; NT 0.1 μg/μl; TSNT 0.01 amol/μl) and aquantitation standard (e.g., TSR8; 0.1 amol/μl).

In a further aspect of the invention, an assay system and apparatus areprovided which allow for high throughput detection of telomeraseactivity. The assay system and apparatus provide for simultaneousseparation of telomerase products from primers and nucleotides inmultiple samples and allows for quantitative detection of the isolatedtelomerase products.

While the methods of the invention are broadly applicable to thedetection of telomerase activity in any sample from any origin, themethods are especially useful and applicable to the detection oftelomerase activity in samples of biological material obtained fromhumans. Such samples will contain cells or cellular materials and willtypically be obtained from humans for the purpose of detecting adiseased state or other medical condition of interest, such as, cancer.Telomerase is not expressed by most normal post-natal human somaticcells, although low levels of telomerase activity can be detected incertain stem cells, activated cells of the hematopoietic system, andfetal tissues, so the presence of telomerase activity in a sample ofhuman somatic tissue or cells indicates that cells of extendedproliferative capacity, such as immortal cells, fetal cells, orhematopoietic cells, are present in the tissue. While not all cancercells express telomerase activity, telomerase expression is required forcells to become immortal. Consequently, the presence of cells withtelomerase activity is associated with many forms of cancer and can alsoserve to indicate that a particularly invasive or metastatic form ofcancer is present.

Thus, the invention provides a method for diagnosis of a condition in apatient associated with an elevated (or reduced) level of telomeraseactivity within a cell. The method involves determining the presence oramount of telomerase activity within the cells of the patient, and themethod is therefore applicable to the detection of elevated (or reduced)levels of telomerase activity associated with, for example, prostatecancer, breast cancer, colon cancer, renal cancer, skin cancer, livercancer, ovarian cancer, cervical cancer, lung cancer, urogenitarycancer, and leukemia, or, in the case of reduced levels, infertility.The method can also be used for testing other diseased states andmedical conditions, e.g., fetal cell testing to detect fetal cells inmaternal blood as an indication of pregnancy or to detect telomerase asa marker for bone marrow proliferative capacity. Whether for diagnosisor other purposes, the method involves determining the presence oramount of telomerase activity within the cells by a telomerase substrateextension reaction, and replicating the extended telomerase substrate,for example, by primer extension, such as in the PCR. These and otheraspects of the invention will be better understood by reference to thefollowing detailed description of specific embodiments together with thedrawings that form part of this specification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a schematic perspective of the Multiplex ElectrophoreticSeparator (MES) apparatus of the invention. The parallel arrows depictthe direction of the electrical field when the electrodes are attachedto the electrical source.

FIG. 1B is a cross sectional view of the MES apparatus.

DESCRIPTION OF SPECIFIC EMBODIMENTS

The present invention provides novel methods and materials for thedetection of telomerase activity. Telomerase synthesizes telomeric DNAat the ends of chromosomes and is believed to be necessary forindefinite proliferation of immortal cells. Analysis of chromosometerminal restriction fragments (TRF) in a wide variety of human celltypes has shown that telomere length and sequence are stably maintainedin immortal cell lines but not in dividing cultures of normal somaticcells. Telomere and telomerase biology are clearly important in themaintenance of the immortal cell state and other biological states.

Thus in one aspect of the invention, a method is provided that involvesthe basic steps of:

(a) incubating a cell sample or an extract therof in a reaction mixturecomprising a telomerase substrate under conditions such that telomerasecan catalyze extension of the telomerase substrate by addition oftelomeric repeat sequences;

(b) replicating the extended telomerase substrate; and

(c) correlating presence of telomerase activity in the cell sample withpresence of the extended telomerase substrate.

The method essentially involves two reactions: (1) telomerase-mediatedextension of a telomerase substrate; and (2) replication oftelomerase-extended substrates. For a more complete understanding of theinvention, one should consider certain global issues relating to (1) thenature of the sample; (2) the important features of the telomerasesubstrate; and (3) the nature of the replication of thetelomerase-extended substrate.

Nature of Sample

Any type of sample can be tested by the methods of the invention.Samples of particular interest include cell samples, which can be tissueor tumor samples, obtained for purposes of diagnostic analysis. Theexpression of telomerase activity in a variety of cells has been studiedand discussed in the scientific literature. Telomerase is expressed notonly by certain pathogens (i.e., malaria, fungi, yeast, and ciliates)but also by immortal human cells, including certain types of tumor andcancer cells, but is not expressed by cells of normal somatic (asopposed to germline or embryonic) tissue, although low levels oftelomerase activity can be detected in stem cells, fetal cells, and incertain activated cells of the hematopoietic system. Consequently,samples can be obtained for the purpose of determining whether atelomerase-expressing pathogen or cancer or tumor cell is present. Forsuch purposes, the sample will often be obtained from a human, but onecan also readily understand that samples tested by the present methodcan be obtained from agriculturally important mammals, such as cattle,horses, sheep, or any other animal of veterinary interest, such as catsand dogs, and from the environment, i.e., for environmental testing forthe presence of pathogens.

In one embodiment of the invention, telomerase activity is assayed invitro, requiring the preparation of a cell extract. Methods for thepreparation of cell extracts are known in the art (for example, seeScopes, 1987, Protein Purification: Principles and Practice, SecondEdition, Springer-Verlag, N.Y.). Preferably, the detergent lysis methodis used which provides more uniform extraction of telomerase even at lowcell numbers. The method involves the steps of: (1) collecting a sampleof cells; (2) lysing the sample in a lysis buffer comprising 0.01 to 5%of a non-ionic and/or a zwitterionic detergent; (3) removing cellulardebris by centrifugation; and (4) collecting supernatant separated fromthe cellular debris. Such a method is illustrated in Example 1, below. Acell extract can also be prepared merely by lysing a cell sample torelease telomerase without further sample preparation.

A wide variety of non-ionic and/or zwitterionic detergents can beemployed in the method. Preferred non-ionic detergents include Tween 20,Triton X-100, Triton X-114, Thesit, NP-40, n-octylglucoside,n-dodecylglucoside, n-dodecyl-beta-D-maltoside,octanoyl-N-methylglucamide (MEGA-8), decanoyl-N-methylglucamide(MEGA-10), and isotridecyl-poly(ethyleneglycolether)_(n), and preferredzwitterionic detergents include CHAPS(3-{(3-cholamidopropyl)dimethylammonio}-1-propane-sulfonate), CHAPSO(3-{(3-cholamidopropyl)dimethyl-ammonio}-2-hydroxy-1-propane-sulfonate),N-dodecyl-N,N-dimethyl-3-ammonio-1-propane-sulfonate, and digitonin,with CHAPS a particularly preferred detergent. While the exact amount ofdetergent is not critical, 0.5% is typically sufficient to observe theenhanced extraction of telomerase activity.

Although the assay of cell extracts is not limited to extracts that havebeen obtained using the detergent lysis method, such extracts arepreferred, especially when telomerase activity is assayed from a singlecell, only a few cells are available or the number of cells expressingtelomerase activity in a sample is very low. The telomerase activityassay of the invention is far superior to the conventional assay indetecting telomerase activity in such circumstances, as well as beingfaster to complete and more efficient.

In another aspect of the invention, the telomerase activity assay isapplied to intact cells. In this embodiment, one treats intact cellswith the telomerase substrate to promote internalization of thesubstrate, following which the substrate is extended if the cellpossesses functional telomerase activity. Internalization of thesubstrates can be achieved using methods known in the art, for example,by passive internalization of substrate oligonucleotides or othernucleic acid added to the media surrounding the cell sample (typicallyat a concentration of 10-100 μM), by microporation using a detergent orStaphylococcus alpha toxins, by employing liposomes (e.g.,LipofectAmine™, Lipofectin™, LipofectAce™ available from BRL), usingbiolistics, or by electroporation. After the target DNA is internalizedby the cell, the sample is incubated to allow any active telomerasepresent in the cell to extend the substrate by de novo synthesis oftelomere repeats. After incubation, the sample is fixed andpermeabilized, for example, by treatment with a protease such asproteinase K, pronase, trypsin, pepsin, or the like. Thetelomerase-extended substrate is then amplified in situ by any ofvarious methods known in the art, for example, using a primer extensionreaction (e.g., employing established PCR or LCR protocols or primed-insitu labelling (PRINS; Koch, J., in "Nonradioactive in situHybridization Application Manual" (1992), Boehringer Mannheim, 31-33) orby other methods as described below. The presence of a signal in a cellduring microscopic examination corresponds to the presence of telomeraseactivity.

Important Features of the Telomerase Substrate

Regardless of the origin of the sample, the sample (or an aliquotthereof) is assayed in a reaction mixture comprising a telomerasesubstrate. The particular telomerase substrate chosen in each case mayvary depending on the type or origin of the telomerase activity forwhich one is testing, or the type of amplification or detection methodemployed. The telomerase activity expressed by one organism may differwith respect to substrate specificity from that expressed by anotherorganism. Consequently, if one is using the present method to determinewhether a cancer cell of human origin is present in the sample, oneemploys a telomerase substrate recognized by human telomerase.

A variety of substrates are known for the telomerases of Tetrahymena,other fungi, mammalian, and human cells and can readily be identifiedfor other types of cells. However, when one employs a DNApolymerase-based primer extension step, the present method requires thatthe telomerase substrate not comprise a complete telomeric repeatsequence to minimize primer-dimer formation. Those of skill in the artwill recognize that the telomeric repeat sequence produced by telomeraseactivity will depend upon the origin of the telomerase. For instance,Tetrahymena telomerase adds repeats of sequence 5'-TTGGGG-3' to the endsof telomerase substrates, while human telomerase adds repeats ofsequence 5'-TTAGGG-3'. Thus, if one is using the present method to assayfor human telomerase activity, the telomerase substrate should be ahuman telomerase substrate lacking the complete repeat sequence5'-TTAGGG-3'. There is no requirement that a human telomerase substratelack a telomeric repeat sequence from an organism that has a telomerasethat adds a different repeat, so long as the presence of that differentrepeat sequence does not produce undesired results, such as excessiveprimer-dimer formation, as discussed further below.

In addition to linear single stranded or duplex nucleic acids, thesubstrate can be a circular plasmid DNA that undergoes linearization ata specific site, either inducibly or spontaneously. Such a plasmidsubstrate is particularly useful for in situ applications. Anillustrative plasmid telomerase substrate is a vector that contains aninsert with a unique restriction site (e.g., Isce I) located 3' to thetelomerase substrate sequence. In this context, "unique" means that therestriction site is not present in the genome of the cell underanalysis. Preferably, the vector is a selectable, multi-copy vector witha mammalian origin of replication. The method can further include asecond expression plasmid that contains a gene coding for a restrictionenzyme specific for the unique site, under the control of an induciblepromoter. The two plasmids are co-infected into the target cell bymethods known in the art, and are replicated. Upon induction of theexpression plasmid product, the restriction enzyme cleaves the DNA ofthe telomerase substrate plasmid at the unique restriction siteresulting in a linearized substrate plasmid, the ends of which arerecognized as a telomerase substrate and can be elongated with TTAGGGrepeats by telomerase.

There is a requirement for the telomerase substrate to lack telomericrepeat sequences in some instances, in particular where the replicationstep of the present method involves the hybridization of a primer orprobe to extended telomerase substrates. For example, in someembodiments, the non-telomerase-mediated primer extension reactioninvolves hybridization of an oligonucleotide primer that hybridizes onlyto extended telomerase substrates. This addition is made underconditions such that, if extended telomerase substrates are present, theprimer binds to the extended substrates and is then extended byenzymatic action. Because telomerase can extend the telomerase substrateonly by the addition of telomeric repeats, the primer will necessarilycomprise a sequence complementary to a telomeric repeat. If thetelomerase substrate employed in the telomerase extension reactioncomprised a complete telomeric repeat, then the primer employed in theprimer extension reaction could hybridize readily to unextendedtelomerase substrate, with potentially negative consequences. Thetelomerase substrate can, however, comprise sequences highly related toa telomeric repeat sequence without compromising the validity of theresults obtained. For instance, an especially preferred human telomerasesubstrate of the invention is oligonucleotide M2, also known as TS,which contains a sequence at its 3'-end that is identical to five of thesix bases of the human telomeric repeat but otherwise contains nocomplete telomeric repeat sequences. There is no requirement that thetelomerase substrate be free of telomeric repeat sequences where thereplication or detection method is not compromised by the presence ofsuch repeats in the substrate, i.e., where primer extension is mediatedby a ligase activity, or replication is achieved by means in whichspecific hybridization of a probe or primer to a telomeric repeatsequence is not problematic.

Replication of Telomerase-Extended Substrates to Enhance Detection

(i) Primer Extension

The primer extension reaction conducted subsequent to the telomerasesubstrate extension serves to amplify the signal produced by thepresence of telomerase activity in a sample (extended telomerasesubstrates) by producing a second signal (extended primers). The primerscan be extended by any means that requires the presence of extendedtelomerase substrates for primer extension to occur; preferred means aremediated by a template-dependent DNA or RNA polymerase, atemplate-dependent DNA ligase, or a combination of the two. With thesemeans, if telomerase activity is present in the sample, an extendedtelomerase substrate is formed and then hybridizes to a primer,providing a substrate for either DNA or RNA polymerase or DNA ligase toproduce a primer extension product.

Once a primer extension product has formed, one can disassociate(typically by heating, but one could also use an enzyme or chemicalprocess, such as treatment with helicase) the extended primer from theextended substrate. If additional primer and primer extension reagent ispresent in the sample, then a new primer/extended telomerase substratecomplex can form, leading to the production of another extended primer.One can repeat the process of primer extension and denaturation severalto many times, depending upon the amount of signal desired. Typically,primer extension and denaturation of extended primer/extended telomerasesubstrate complexes will be performed at least 5, 10, 15, 20 to 30 ormore times. Moreover, if a second primer complementary to the 3'-end ofthe extended primer is present in the reaction mixture, one can increasethe signal (both extended primer and also additional extended telomerasesubstrate) dramatically. Unextended telomerase substrate still presentin the reaction mixture during the primer extension step can function assuch a second primer.

Those of skill in the art will recognize that if the primer extensionreagent is a DNA polymerase, and a second primer is present, one has therequisite components for a polymerase chain reaction, more fullydescribed in U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188,provided the appropriate buffer and nucleoside triphosphates are presentin the reaction mixture. PCR amplification is a preferred mode forconducting the primer extension reaction step of the present inventionand dramatically increases sensitivity, speed, and efficiency ofdetecting telomerase activity as compared to the conventional assay. Theprotocol is termed "TRAP" for Telomeric Repeat Amplification Protocoland is illustrated, inter alia, in Example 2. The telomerase substratecan also conveniently serve as a PCR primer (termed the "upstreamprimer"), although many other primer sequences can also be used. Thesequence of the other primer is chosen to avoid annealing of thetelomerase substrate and the primer, because even minor levels ofprimer/telomerase substrate annealing can yield early cycle PCR productsidentical to telomerase products (e.g., TS plus (5'-AG GGTTAG!_(n) -3'),where n equals 1, 2, 5, 10, or more. In subsequent cycles, theseproducts could serve as template for the production of PCR products,potentially resulting in a false positive result.

The present invention provides a variety of oligonucleotide primers andtelomerase substrates for use in the PCR-based embodiment of the presentinvention. One such primer (termed the "downstream primer") isdesignated "CX" and is composed of sequences complementary to threeimperfect telomeric repeats and one perfect repeat, 5'-(CCCTTA)₃CCCTAA-3' (SEQ ID NO:1). The single nucleotide difference in three ofthe repeats compromises the capacity of CX to anneal to the telomerasesubstrate TS (which, as noted above, contains 5 of 6 nucleotides of atelomeric repeat) by creating a 3' mismatch in the TS/CX duplex, therebyminimizing the formation of non-specific PCR products, such asprimer-dimer. Any possible alignment between these primers (CX and TS)nucleated by the telomeric sequence complementarity leads to a duplex inwhich the recessed 3' nucleotide is mismatched and so is not efficientlyextended by polymerase.

As the CX primer demonstrates, and as those of skill in the art willrecognize upon review of this disclosure, a primer with sequences"complementary to a telomeric repeat" includes a primer that may containone or more mismatched bases with respect to the telomerase substrateextension product to which the primer is intended to hybridize. Thenumber of mismatches that can be tolerated within this definition canvary depending upon the length and sequence composition of the primer,the temperature and reaction conditions employed during the PCR step,the purpose for which the assay is conducted, and the results desired.

In addition to primer CX, the present invention provides severalmodifications of a basic PCR that, while not necessary to obtain thebenefits of the present method, can greatly enhance the specificity,sensitivity, and efficiency of the present method for some applicationsand in certain embodiments. For instance, one important modification tothe in vitro method relates to the buffer: the present inventionprovides a buffer in which both telomerase activity and DNA polymeraseactivity can be observed. The use of such a buffer allows the artisan toconduct both the telomerase substrate extension reaction and a DNApolymerase-mediated primer extension reaction in the same reactionvessel, for example, in a tube (see Example 2).

Another modification relates to the use of relatively shortoligonucleotides that are complementary to either the telomerasesubstrate or the return primer in the reaction mixture. These shortoligonucleotides are designed to have a melting temperature (withrespect to the primer or telomerase substrate to which the shortoligonucleotides hybridize) about 10° C. lower than the annealingtemperature of the primers used in the primer extension step and toprevent primer-dimer formation and/or non-specific primer extension,particularly at low temperatures. The short oligonucleotides melt awayfrom their complementary oligonucleotides at temperatures just below theideal annealing temperatures for the primer extension step, preventinginappropriate primer extension at lower, non-specific temperatures.Given that the short oligonucleotides are not intended to serve asprimers for DNA synthesis, the 3'-end of the short oligonucleotide canbe blocked to prevent addition of nucleotides to the shortoligonucleotide. If the short oligonucleotide is designed to hybridizeto the primer, then the 3'-end of the short oligonucleotide should beblocked (e.g., with biotin, phosphate, digoxigenin, a fluorescein or anamino group) to prevent the short oligonucleotide from serving as atelomerase substrate.

A variety of other reagents and formats can be employed to ensure a highdegree of specificity, including: (1) the use of T4 gene 32 protein(available, e.g., from Boehringer Mannheim); (2) the use of TaqStart™antibody (available, e.g., from Clontech); and (3) the separation of theprimer from the other reaction components by a wax barrier (e.g.,Ampliwax™, available from Perkin Elmer) that melts only after thereaction mixture is heated at the end of the telomerase-mediatedextension reaction. The purpose of the wax barrier is to separate thetelomerase extension reaction from the amplification reaction. Thus, asone example, and there are many examples, the DNA polymerase can besealed under a wax layer thus separating it from other reactioncomponents. Alternatively, the primer can be sealed under a wax layer orbarrier at the bottom of a tube with the other reaction componentspositioned on top of the barrier.

For ease of preparation, reaction components can be attached to solidmatrices, such as polystyrene beads of about 1 micron to about 5millimeters in diameter; plates or the wells of a microtiter plate suchas those made from polystyrene or polyvinylchloride; glass beads;magnetic particles; polysaccharides; or other surfaces that can becoated, e.g., with primer. The primer is typically affixed to the solidmatrix by adsorption from an aqueous medium although other modes ofaffixation, as is well known to those of ordinary skill in the art, canalso be used. For example, the solid surface is contacted with asolution of the primer and dried until the surface is coated with anappropriate amount of primer. The amount of primer coated on the solidsurface can be varied by adjusting the concentration of primer in thecontacting solution. The primer-coated solid matrix is then covered withhot molten wax that is left to solidify. The wax barrier thus isolatesthe primer from the other reaction components (e.g., the telomerasesubstrate, dNTPs, buffer, DNA polymerase or ligase) until a temperatureis reached at which the wax melts. These formats ensure that the returnprimer will be accessible to the other reagents only at temperaturesthat ensure highly specific nucleic acid basepairing and so reducesnon-specific primer extension and primer-dimer (composed of a primer andan unextended telomerase substrate) formation. In addition, tis formatallows one to conduct the activity assay in a single reaction tube andprovides a convenient format for packaging the reaction components.Thus, one useful kit of the invention comprises a reaction tube or othersolid support having a primer or polymerase separated from thetelomerase reaction buffer and/or other reagents by a wax barrier.

The primer extension methods of the present invention have been used totest for telomerase activity in human cell lines and normal somaticcells as illustrated in Examples 2. Telomerase-positive extracts fromhuman 293 kidney cells were produced routinely from 10⁵ cells, asassessed by TRAP assay, with a lower limit for the conditions employedin this particular example of 10² cell equivalents for detection oftelomerase activity. These results demonstrate at least 100-foldimprovements in both extraction efficiency and telomerase activitydetection when compared to conventional methods and together increasecurrent detectability of telomerase activity by a factor of at least10⁴. The telomerase activity assay method of Example 2 has been used totest for telomerase activity in various immortal cell lines and normalsomatic cell cultures from different tissues and individuals, asillustrated by Example 3 below. As shown in Example 3, the difference intelomerase activity between immortal and normal somatic cells wasestimated to be at least 1000-fold, supporting a direct role fortelomerase in telomere dynamics in human cells.

Those of skill in the art will recognize the detection limits notedabove are valid only if one employs merely routine procedures. Thepresent method can be used to detect telomerase activity in a singlecell, provided one is willing to use effort somewhat greater than whatis typically considered routine, primarily for the single cell isolationstep. One can increase the time of the telomerase-mediated extensionstep, increase the purity of the test extract for telomerase, increasethe amount of labels used in the assay, and increase the number ofprimer extension cycles to increase the sensitivity of the assay todetect telomerase activity in a few cells or a single cell. Example 11illustrates this aspect of the invention.

The PCR-based embodiment of the present invention offers significantimprovements over currently available methods for measuring telomeraseactivity in a sample. Other novel variations of the present method,however, also offer significant advantages. In particular, the presentmethod can be used to quantitate the telomerase activity in a sample byproviding the number of telomerase products generated. To understand thenature of these improvements, however, one should first consider morecarefully the ladder of bands produced upon gel electrophoresis oftelomerase extended substrates. Such results reflect the number ofrepeats added by telomerase during the telomerase-mediated extensionreaction, but in certain PCR-based embodiments of the presentinventions, some of these products can result from staggered binding ofprimers during the PCR amplification steps.

The phrase "staggered binding" refers to the binding of a primer to asequence in an extended telomerase substrate in a manner that leaves the3'-end of the extended telomerase substrate recessed and thereforeavailable for extension by DNA polymerase. In such a configuration, DNApolymerase can add nucleotides to the 3'-end of the extended telomerasesubstrate, creating molecules longer than those produced in thetelomerase-mediated extension step. To determine whether staggeredbinding was occurring in reactions such as those described in Example 2,synthetic oligonucleotides representing discrete telomerase extensionproducts, e.g., TS+4 (TS plus four telomeric repeats), were used todevelop specific amplification conditions. Even under high stringency,staggered annealing of the downstream primer occurred (e.g., annealingby 3 of the 4 repeats). Hence PCR amplification of a discrete telomeraseextension product yielded a six nucleotide ladder of PCR productsincreasing in size up to the limit of gel resolution. Thus, TRAP assayproducts produced using a primer such as CX are not directly reflectiveof the length distribution of telomerase products generated in thetelomerase substrate extension step, due to the staggered binding ofprimers to templates during the primer extension reactions.

In some cases, however, for example in in situ telomerase assays, it canbe advantageous to have staggered binding resulting in larger moleculesthat prevent leakage of the telomerase products out of the cell.However, in in vitro assays, it may sometimes be preferable that suchinteractions be prevented by employing a novel "anchored" primer of theinvention as the downstream primer in the assay. For purposes of thepresent invention, an anchor sequence is a 5'-terminal sequence of a PCRprimer that is a non-telomeric repeat sequence (a sequence neithercomplementary nor identical to a complete telomeric repeat sequence) andthat prevents the PCR product from "growing" on itself, for example asobserved when the primer pairs TS/(CTR)₄ or TS/CX are employed. Thus,such an oligonucleotide can comprise a 6 nucleotide anchor sequence(although the length is not critical and can be 3 to 5 to 15 to 30 ormore nucleotides) at its 5'-end followed by three repeats of CTR (C-richtelomeric repeat; 5'-CTAACC-3') sequence (e.g., the ACT primer;5'-GCGCGG CTAACC!₃ -3'; SEQ ID NO:2 is an anchored primer of theinvention).

A wide variety of anchor sequences can be employed. In one embodiment,the anchor sequence is the sequence of the telomerase substrate used inthe telomerase-mediated extension step of the method, providing a"TS-anchored" primer (note that, in this context "TS" represents anytelomerase substrate lacking a complete telomeric repeat sequence). Theanchored primer would thus comprise, in the 5'-to-3' direction, atelomerase substrate sequence and two or more complementary copies ofthe telomeric repeat sequence. By employing such a primer, one canpractice the present method in what is essentially a "one primer" mode,because after the first round of primer extension, excess unextendedtelomerase substrate in the reaction mixture can prime the synthesis ofboth strands of the duplex formed as a result of the first round ofprimer extension.

By using, for example, the primers TS (5'-AATCCGTCGAGCAGAGTT-3'; SEQ IDNO:3) and ACT (or another anchored primer) in the TRAP assay, one candeduce the Most Processive Product (MPP) of the telomerase in a givenextract. The use of an anchored primer such as ACT prevents the growthof telomerase products into longer versions during PCR. With the ACTprimer, the slowest migrating band reflects directly the length of theMPP of the original telomerase products before the PCR. Without suchprimers, multiple cycles of primer extension and product denaturationcan yield primer extension products that comprise many more telomericrepeats than present in the telomerase-extended telomerase substratesoriginally present in the reaction mixture after the telomerasesubstrate extension reaction. The ACT primer is particularly preferredfor purposes of the present invention in that it is more resistant tothe types of primer-dimer interactions observed between TS and primerssuch as CX or CTR₄. Alternatively, a hybrid oligonucleotide can be usedas a return primer. The hybrid has an anchor sequence followed by aprimer-based sequence that contains mismatches in the complementarytelomeric repeats, for example, ACX 5'-GCGCGG CTTACC!₃ CTAACC-3' (SEQ IDNO:4) that has mismatches in 3 of 4 complementary telomeric repeats.This results in a primer that has the ability to destabilizeprimer-dimer formation (like a CX primer) and to predict the mostprocessive telomerase product from the TRAP assay (like an ACT primer).Furthermore, the resulting ACX is more resistant to primer-dimerformation than either the ACT or CX primer. The utilization of the ACXprimer in the TRAP assay provides similar benefits as the wax-barriermethodology in preventing primer-dimer formation, but simplifies theanalysis, manufacture, and performance of the TRAP assay.

The TRAP assay can be further improved by reducing non-specific,template-independent, PCR artifacts (e.g., primer-dimer) by means otherthan or in addition to oligonucleotide selection and the use of ahot-start wax barrier. For example, the addition of dimethyl sulfoxide(DMSO), optionally with glycerol, to the TRAP assay buffer destabilizesthe interactions between the telomerase substrate primer (e.g., TS) andthe return primer (e.g., CX, ACT) thereby increasing the reliability ofthe TRAP assay. Similarly, the use of a DNA polymerase or fragmentthereof (e.g., the Stoffel fragment of AmpliTaq™ DNA polymerase; PerkinElmer) that lacks a 5' to 3' exonuclease activity can be employed toprevent primer-dimer artifacts. When a primer, such as CX or a CX-basedprimer, hybridizes to a template (e.g., TS), the 3' mismatch of theprimer should prevent primer extension. However, DNA polymerases withinherent 5' to 3' exonuclease activity are able to remove the 3'mismatched nucleotide and extend the primer. In contrast, a DNApolymerase or fragment that lacks a 5' to 3' exonuclease activity isunable to cleave the mismatched nucleotide and thus helps preventmisextension of primers and primer-dimer artifacts.

The present invention also provides a variety of means to quantitate theamount of telomerase in a sample, although for most purposes, aqualitative result (telomerase activity present or absent) issufficient. One important means for obtaining quantitative informationis the use of a control oligonucleotide template added to each reactionmixture in a known amount, as illustrated below in Example 4.

An illustrative competitive control oligonucleotide of the inventioncomprises, in 5'-to-3' order, a telomerase substrate sequence, a spacersequence (preferably 3 nucleotides in length, but which can be anysequence of nucleotides or length; a length of 3 nucleotides ensuresthat the internal control is different from that from the extendedsubstrates, and a telomeric repeat sequence (typically present inmultiple, e.g., 2 to 50, copies). Of course, an oligonucleotidecomplementary to the control sequence defined above can also serve asthe control sequence, or a double-stranded control nucleic acid, orplasmid with a double-stranded nucleic acid insert can be employed. Useof this internal control not only facilitates the determination ofwhether the assay was conducted properly but also facilitatesquantitation of the telomerase activity present in the sample.

Alternatively, one can add a control nucleic acid of any sequence to thereaction mixture in known amounts and amplify the control with primersdifferent from those used to amplify the extended telomerase substrate(non-competitive internal control). The control oligonucleotide and/orthe primers used to amplify the control oligonucleotide can be labelledidentically to or differently from the label used to label thetelomerase extension products. A preferred internal controloligonucleotide comprises a combination of the controls described abovewhere, in the PCR embodiment of the invention, the internal controlcompetes with the telomerase extension product for only one primer andis thus termed a semi-competitive control. Such a control comprises, in5'-to-3' order, a sequence that is not a substrate for telomerase or atelomeric repeat, or a complementary sequence thereof followed by atelomeric repeat sequence. One can also design internal controls thatcan be amplified by a single primer, as is evident to those of ordinaryskill in the art. An alternative semi-competitive control comprises, in5'-to-3' order, a telomerase substrate sequence followed by a sequencethat is neither a substrate for telomerase nor a telomeric repeat or acomplementary sequence thereof. The control can also be designed to beseparated easily from the TRAP products for quantitation. An example ofsuch a semi-competitive internal control is5'-AATCCGTCGAGCAGAGTTAAAAGGCCGAGAAGCGAT-3' (SEQ ID NO:5; TSNT) that canbe amplified by the TS telomerase substrate primer and the NT primer5'-ATCGCTTCTCGGCCTTTT-3' (SEQ ID NO:6). The NT primer is not a substratefor telomerase. The TSNT oligonucleotide is employed in a TRAP assaywith TS, ACX (or any other return primer) and NT, and the resulting 36bp control duplex DNA is easily distinguished from the telomeraseextension products, the smallest of which is 50 bp. The controloligonucleotide can also be conveniently packaged into a kit with otherreaction components.

To detect the presence of a nucleic acid in a sample, the TaqMan™(Perkin Elmer) detection system can be employed. This system is suitablefor use in the telomerase assays of the invention and provides a rapiddetection method that is non-radioactive and readily modified to amultiwell system. A target specific probe that possesses both afluorescent reporter dye tag and a quencher dye tag is incorporated intothe primer extension reaction (e.g., PCR amplification). Although thereis no precise limitations on the positions of these tags, it will beapparent to one of ordinary skill in the art that particular positionsmay be preferable to others; for example, the tags are preferablypositioned 6-8 nucleotides apart. The TaqMan™ probe hybridizes to thetarget sequence at an internal site under primer extension conditionsand, if the primer is extended by the action of a DNA polymerase having5'-3' exonuclease activity, the 5'-3' exonuclease activity of thepolymerase degrades the hybridized probe freeing the reporter dye/dNTPfrom the proximity of the quencher dye. The increase in the freereporter dye/dNTP complex results in an increase in fluorescence that isproportional to the amount of amplified product (Livak et al., January1995, Research News, Perkin Elmer Corporation, 1-5; Lee et al., 1993,Nucl. Acids Res. 21:3711≧3766). In a typical TaqMan™ PCR application,where the target is generally a double stranded DNA of 100 bp-1 kb inlength, selection of three specific hybridization sites (one site forthe forward primer, one site for the return primer and one site for theTaqMan™ probe) is easily accomplished. However, in the TRAP assay, thechoice of specific hybridization sites available for the TaqMan™ probeand the two primers is limited. These sites comprise the telomerasesubstrate sequence (e.g., TS; 5'-AATCCGTCGAGCAGAGTT-3'; SEQ ID NO:3),and the telomeric repeat sequences (e.g., TTAGGG), or theircomplementary sequences, with or without mismatches. For example, aTaqMan™ probe that comprises C-rich telomeric repeat (CTR; 5'-CCCTAA-3')sequences can be used (e.g., a probe that comprises four repeats of CTR;this probe is termed CTR₄). Although TaqMan™ probes are generallyblocked at their 3' ends, and thus cannot be elongated during PCRamplification, the CTR probes could compete with the ACT primer (orother return primers) as they hybridize to the same sites, which canlead to a reduction in PCR efficiency. Furthermore, because the probecan anneal to the telomerase substrate, such as TS, the use of hot-startPCR methodology in the assay may be useful; this can readily beaccomplished by separating the probe and the return primer with a waxbarrier from the remaining reaction components.

A preferred TaqMan™ probe consists of a sequence complementary to thetelomerase substrate; therefore such a probe does not compete witheither the forward or return primers, and thus does not result inprimer-dimer formation. Such a probe can form a duplex with the forwardprimer (e.g., TS), which can decrease PCR efficiency during exponentialamplification. However, telomerase can recognize and extenddouble-stranded substrates (see Example 8), and the reaction can proceedin the presence of forward primer-probe duplexes.

Alternatively, a TaqMan™ probe that consists of a sequence complementaryto the 3' region of the forward primer, followed by a telomeric repeatsequence (e.g., CTR sequence), can be used. Such a probe specificallyhybridizes to the junction between the forward primer and the telomericrepeat sequence and reduces not only competitive effect with the returnprimer but also forward primer-probe duplex formation. With such aprobe, generation of primer-dimer artifacts can be avoided by usinghot-start TRAP methodology. For example, a probe comprising the sequence5'-AACCCTAACCCTAACTCTGCT-3' (SEQ ID NO:7), corresponding to the junctionsequence between the 3' end of TS and the telomeric repeats of thetelomerase product, can be used. Alternatively, mismatches can beintroduced into such probes to minimize potential interference with thetelomerase substrate extension reaction, i.e., by minimizing probebinding to TS during the extension step. For example, probes having thesequence 5'-CCTAACCCTAACCCCACTATGCT-3' (SEQ ID NO:8) or5'-CCTAACCCTAACCCTGTATATGCT-3' (SEQ ID NO:9) can be used in thisembodiment. Conditions are selected to allow the probe to bindpreferentially to the extended telomerase substrate during the PCRreaction.

A TaqMan™ probe consisting of the telomerase substrate sequence ortelomere repeat sequences (e.g., 5'-TTAGGG-3') can also be used in theTaqMan™ detection system. However, in addition to the potentialformation of primer-dimers and primer competition discussed above, theseprobes may compete with the telomerase substrate for telomerase,although competition can be minimized using hot start methodology.

In another embodiment of TaqMan mediated extension, reporter andquencher dyes are present at the two ends of a return primer with a 3'mismatch, as exemplified by the primer MACX, which has the sequence5'-GCGCGG CTTACC!₃ CTAACCAAT-3' (SEQ ID NO:10), without 3' blocking ofthe primer. When such a primer is used in the TRAP assay with athermostable DNA polymerase with proof-reading capability, themismatched nucleotide at the 3' end of the primer is cleaved by theexonuclease activity releasing the reporter dye from the quencher priorto extension. Thus, any amplification using such a primer results in afluorescent signal. This embodiment of the invention is not limited tofluorescence quenching, as other proximity indicating signals can beused; for example, a probe can be labelled with a radioactive label anddetected with a scintillant.

Those of skill in the art recognize that the method of the invention caninvolve the correlation of telomerase activity in a sample with theformation (presence in the reaction mixture) of duplex nucleic acidscomposed of extended telomerase substrates annealed to extended primers.One can infer the presence of such molecules by the presence of either(1) an extended telomerase substrate; (2) an extended return primer; (3)a duplex nucleic acid comprising both (1) and (2); or (4) hybridizationof a probe to any of the foregoing. In any event, however, one willtypically make this correlation by detecting the presence of extendedtelomerase substrates and/or primers via a label incorporated into orattached to one or more of the reaction products, although the Taqman™detection method described above is perhaps an exception to this rule.

While the PCR-based embodiment of the present method has been describedin detail above and is exemplified in the Examples below, the presentmethod can be practiced using any method of primer extension to providetarget amplification or with a method that provides for signalamplification or both, as described below. In addition, while PCRprovides for exponential accumulation of primer extension products, evenlinear accumulation of primer extension products can provide usefulresults. Thus, one can use a single primer and merely make many copiesof the telomerase-extended substrate.

Moreover, such copies can be made by means other thanpolymerase-mediated primer extension, as described more fully below. Onesuch method is the ligase chain reaction (Barany, 1991, Proc. Natl.Acad. Sci. USA 88:189-193). Copies of the telomerase extension productscan be made using DNA ligase to ligate together two oligonucleotideshybridized to the extended telomerase substrate. If, as in PCR, theduplex nucleic acid is then denatured, then one can repeat the processof ligation and denaturation many times to accumulate many complementarycopies of the original extended telomerase substrate. If oneadditionally adds two other oligonucleotides complementary to the copyproduced by ligation of the first two oligonucleotides on the extendedtelomerase substrate and selects those oligonucleotides such that DNAligase can ligate the two together to form an identical (as opposed tocomplementary) copy of the original extended telomerase substrate, thenone has the basic components of an LCR. To illustrate, one could employLCR in the present method using the following four oligonucleotide"ligomers": ##STR1##

The LC and CLT ligomers will anneal to an extended telomerase substrateand then be ligated with DNA ligase to form a template for ligation ofthe LTS and LG ligomers. These ligomers have been selected so that notwo ligomers can anneal to form a duplex nucleic acid that can be joinedto another duplex nucleic acid in the mixture by the blunt-end ligationactivity of DNA ligase. A wide variety of such ligomers can be used inthe method to minimize template-independent product formation. LCRamplification of telomerase extension products produces an amplifiedproduct of uniform size and so is conducive to quantitative analysis.Furthermore, a combination of a thermostable polymerase and a ligasewith primers, such as, for example TS, LC, and CLT, can be used toamplify telomerase-extended substrates.

(ii) Oligonucleotide Proximity Assay

In a further aspect of the invention somewhat related to the LCR methoddescribed above, oligonucleotides complementary to adjacent portions ofthe telomerase extension product (e.g., LC and CLT) are employed todetect the presence of telomerase extension product. Theoligonucleotides are constructed so that when annealed to the telomeraseextension product, the 5'-end of one oligonucleotide can be ligated tothe 3'-end of the other. One of the oligonucleotides is labelled with afluorescent "reporter" label and the other with a "quencher" label. Forexample, the components can both be fluorescence emitters with theabsorbance spectrum of the first being selected to overlap with theemission spectrum of the second; an example of such a pair would befluorescein and rhodamine. Upon annealing of the oligonucleotides to thetelomerase product, the quenching effect resulting from the proximity ofthe reporter to the quencher can be detected as an indication oftelomerase extension products. Subsequent ligation of the annealedoligonucleotides is required for further amplification by LCR, althoughligation is not required for detection using the assay.

This detection system is not limited to fluorescence and quenching butcan be used with probes comprising any two components that interact in adetectable manner through adsorption, modulation, or emission ofelectromagnetic or nuclear radiation. Detection can, for example, bemediated by chemical, enzymatic or radiation events. For example, aradioactive label and a scintillant, or an enzyme pair in which theproduct of one enzyme is a substrate for the second can be used toprovide a proximity signal. Any proximity indicating pair resulting in adetectable signal can be used; detection can be fluorometric,radiometric, or colorimetric, for example.

(iii) RNA Polymerase-Mediated Replication

In one aspect of the invention, telomerase extended products arereplicated by means of the action of an RNA polymerase. A variety ofmethods for replicating nucleic acids using an RNA polymerase are known,e.g., nucleic acid sequence-based amplification (Compton, 1991, Nature350:91-92), self-sustained sequence replication (Guatelli et al., 1990,Proc. Natl. Acad. Sci. USA 87:1874-1878), and strand displacementamplification (Walker et al., 1992, Proc. Natl. Acad. Sci. USA89:392-396). In a preferred embodiment, an RNA polymerase that utilizesa single stranded DNA template (e.g., N4 RNA polymerase) is employed tosynthesize an RNA copy from a single-stranded DNA template using apromoter sequence at the 5' end of the template. The telomerasesubstrate can comprise a promoter sequence operably linked to its 5' endor the promoter can be ligated to the substrate after extension of thesubstrate and prior to replication with the RNA polymerase. Many RNAtranscripts can be generated from a single DNA template therebyincreasing the number of the target molecules. One can optionally employa reverse transcriptase to make DNA copies of the RNA transcript.

Alternatively, the method employs a non-telomeric telomerase substratesequence (e.g., TS) that can be extended by telomerase and, a returnprimer, e.g., CTR₃ (comprising 3 repeats of the CTR sequence) that iscomplementary to telomeric sequences. A DNA polymerase (e.g., Taqpolymerase, Klenow fragment, Stoffel fragment of AmpliTaq™ polymerase)is then used to synthesize a cDNA complementary to the telomeraseextension product. An RNA polymerase that recognises a double strandedsubstrate (e.g., T7 polymerase, T3 polymerase, SP6 polymerase) is thenused to synthesize multiple RNA copies of the duplex telomeraseextension product as directed by a promoter sequence incorporated intothe 5'-end of the telomerase substrate or return primer. Any of avariety of promoters, e.g., T7, T3, SP6 promoters, can be used for thispurpose. The promoter sequence can be present during the telomeraseextension step or ligated at a later stage to the extension products.

As noted above, amplification can also be achieved by using nucleic acidsequence-based amplification (NASBA). In this embodiment, an RNApolymerase (such as T7 RNA polymerase) synthesizes RNA copies of theextended telomerase substrate essentially as described above. A reversetranscriptase is used to synthesize DNA copies of the RNA, RNaseHdegrades the RNA strand and the single stranded DNA acts as a templatefor RNA synthesis, thus providing cyclic amplification. Alternatively,reverse transcriptase can be used to synthesize cDNAs, or RNA polymerasecan be used to extend primers, and the products can be amplified byprimer extension (e.g., with PCR). These and other variations of thepresent method will be apparent to those of skill in the art uponconsideration of this disclosure. In these embodiments, the presence andlevel of telomerase activity is correlated to the presence of RNA copiesof the extended telomerase substrate. As in other embodiments, a widevariety of primers can be designed (for example, to decreasebackground), as would be apparent to one of ordinary skill in the art.

(iv) Branched DNA-Mediated Replication

In another embodiment, telomerase extension products are either firstreplicated and/or then detected using branched DNA (bDNA) signalamplification (Urdea, 12 Sep. 1994, Bio/Tech. 12:926-928; U.S. Pat. No:5,124,246) which involves amplification of the signal produced uponprobe hybridization to a target nucleic acid. The assay for detectingtelomerase activity with bDNA can be carried out in a multi-well plate,a format that is particularly useful for screening, because the assay issimple to perform with multiple samples, and commercial hardware isavailable. Furthermore, conditions can be chosen to allow quantitativedetection of telomerase activity. Any telomerase substrate (e.g., TSoligonucleotide 5'-AATCCGTCGAGCAGAGTT-3'; SEQ ID NO:3) can be used, andthe substrate is incubated with a cell extract, allowing any telomerasepresent to extend the substrate (optionally bound to a solid support tofacilitate detection) with the addition of telomeric repeats. In oneembodiment, the substrate is linked at its 5' end to a well of amulti-well plate (or other solid surface) using conventional chemicaltechniques. Multi-well plates with linked oligonucleotides are alsoavailable commercially (Chiron Corp.). Alternatively, the telomerasesubstrate is bound by hybridization to a complementary oligonucleotidebound to the solid surface. The telomerase extension reaction can occuron bound oligonucleotide substrate or on free oligonucleotide substratethat is bound at a later stage.

The bDNA probe is comprised of a hybridizing portion complementary tothe telomeric repeats (e.g., 5'-(CCCTAA)_(n) -3' or its permutations)and so hybridizes with extended telomerase substrates. The probe furthercomprises a branched region that provides multiple secondary probebinding sites. After washing to remove unbound probe, a labelledsecondary probe specific for the branches of the bDNA is hybridized tothe bDNA and is detected via the label.

The artisan recognizes that this format is amenable to many variations;for example, the telomerase substrate can be immobilized after extensionby telomerase by capturing the telomerase extension products byhybridization to immobilized oligonucleotides complementary to telomericrepeats and detecting the products by hybridization to a probecomplementary to the telomerase substrate. The signal increases indirect proportion to the secondary probe-accessible-sites on the bDNAmolecule, thus a rare population of target nucleic acids can be detectedby bDNA hybridization. Sensitivity can be further enhanced by probingthe telomeric-repeat-complementary-bDNA (or telomerasesubstrate-complementary-bDNA) with a secondary bDNA probe specific forthe branches of the primary bDNA probe (and a tertiary probe specificfor the secondary probe, etc.), thereby presenting more numeroushybridization sites for the labelled probe.

The use of bDNA to probe for extended telomerase substrates is notlimited to use with cell extracts but can also be applied to the in situmethodology of the present invention. Extended telomerase substrates incells fixed onto a microscope slide, for example, can be probed withbDNA instead of conventional linear nucleic acid probes. However, tofacilitate the internalization of the bulky bDNA probes, shorter branchlengths are preferred. Thus, for in situ detection using bDNA, thebranches are usually less than about 60 nucleotides in length,preferably less than about 40 nucleotides in length. The improved probeuptake overcomes any decrease in sensitivity of the assay that may occurresulting from shorter branch length. Furthermore, the combination of asecondary bDNA probe specific for the branches of the primary bDNAprobe, both bDNA probes having short branches, provides additionalsensitivity. The bDNA methodology can also be applied to the detectionof primer extension products, as would be understood by one of ordinaryskill in the art upon reading this disclosure.

Signal amplification can be achieved by using a probe other than bDNAwhich hybridizes to a target nucleic acid, and probe detection,including bDNA probe detection, can be used in many of the embodimentsof the invention. For example, a telomerase substrate can be immobilizedto a solid surface, e.g., a well of a microtiter plate, a tube, orbeads. The telomerase assay is employed to extend the telomerasesubstrate with telomeric repeats (e.g., TTAGGG). The reaction can bestopped, if desired, by washing the solid surface to remove solublereactants, by the addition of denaturing amounts of detergent ordivalent cation chelators, by heating, or by other means. Extendedtelomerase substrate is then probed with a labelled nucleic acidcomplementary to the telomeric repeats. Typically the nucleic acid probe(DNA, RNA, or peptide nucleic acid (PNA) or other nucleic acidanalogues) is directly labelled, although hybridization to a furtherlabelled probe is possible, as is recognized by the artisan. Aparticularly preferred probe is a polybiotinylated nucleic acid that canbe detected by tyramide signal amplification, as described in U.S. Pat.No. 5,196,306. Horseradish peroxidase (HRP)-linked streptavidin binds tothe biotin, and the HRP catalyzes the deposition of activated tyramidemolecules labelled with fluorophores, biotin, or HRP, for furtheramplification, and thus the covalent deposition of fluorophores, biotinor HRP to the solid surface. The deposited labels can be detected bystandard techniques.

Reagents

While the disclosure above and Examples below illustrate the inventionwith results obtained using oligodeoxyribonucleotide telomerasesubstrates, probes, controls, and primers or ligomers, the presentinvention is not so limited. Thus, one can employ oligoribonucleotidesor oligonucleotides that comprise one or more modified (i.e., syntheticor non-naturally occurring) nucleotides as probes or primers. Usually,nucleotide monomers in a nucleic acid are linked by phosphodiester bondsor analogues thereof. Analogues of phosphodiester linkages includephosphorothioate, phosphorodithioate, phosphoroselenoate,phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate,phosphoramidate, peptide, and the like linkages.

For example, PNA is an oligonucleotide with peptide bonds instead ofphosphodiester bonds in its backbone. Because a PNA has no charge, a PNAhas a higher binding affinity than a deoxyribonucleic acid. As anotherexample, a phosphorothioate oligonucleotide having a telomeric ornon-telomeric sequence can be prepared by methods known in the art andused as a telomerase substrate during the telomerase reaction. UnlikeDNA polymerase, telomerase can recognize and extend phosphorothioateoligonucleotide substrates. The products of the telomerase reaction canthen be detected by the methods described herein, except thatamplification of an extended telomerase product using phosphodiesterprimers and a polymerase is asymmetrical unless another primer is added.Polymerases cannot utilize phosphothioate oligonucleotides as primers,so primer-dimer artifact formation is decreased in such an assay,although, compared to exponential amplification of the telomeraseproducts, sensitivity of the assay may be compromised unless anotherprimer is added. Sensitivity can be improved in this embodiment by usingPCR-independent methods of replication or detection, such as by the useof branched DNA probes, as described above.

Those of skill in the art will recognize that the reagents employed arecommercially available or, in the case of the oligonucleotides, can beprepared using commercially available instrumentation, and that a widevariety of DNA polymerases, antibodies, and single-strand DNA bindingproteins can also be employed.

Detection of Replicated Telomerase-Extended Substrates

Regardless of the nature of the replication reaction, and as also notedabove, the various reagents of the invention can be labelled tofacilitate identification of telomerase-extended telomerase substratesor nucleic acids replicated therefrom in a reaction mixture. Forinstance, one can use one or more labelled nucleoside triphosphates, alabelled primer, or a labelled telomerase substrate (or a combination ofthe same) and monitor incorporation of the label into telomerasesubstrate or primer extension products. The internal control, if any,can also be labelled with the same or a different label. Any of a widevariety of labels can be used for purposes of the present invention.Such labels include fluorescent (e.g., fluorescein-5-isothiocyanate(FITC) and rhodamine), phosphorescent, chemiluminescent, enzymatic, andradioactive labels, as well ws various chromophores. A preferredfluorescent label is an intercalating dye. A particularly preferredfluorescent dye is SYBR Green I that exhibits enhanced fluorescence whenbound to double-stranded nucleic acids but only minimal fluorescencewith single-stranded DNA or RNA. Alternatively, the label can merely bean unlabelled "tag", which in turn is recognized by a labelled moleculethat binds to the tag. For instance, one can use biotin as the tag, useavidinylated or streptavidinylated horseradish peroxidase ("HRP") tobind to the tag, and then use a chromogenic substrate (e.g.,tetramethylbenzamie, TMB) to detect the presence of the HRP. In similarfashion, the tag can be an epitope or antigen (e.g., digoxigenin), andan enzymatically, a fluorescently, or a radioactively labelled antibodycan be used to bind to the tag. A further example utilizes telomericrepeat binding proteins that are known in the art. Such proteins havebeen identified as binding either to double-stranded or single-strandedtelomeric repeats and native or recombinant proteins can be used.Typically, such proteins would be purified for use and detected byvirtue of a label attached to, or an antibody specific for, theparticular protein.

Detection of the label may involve additional steps, depending on theneeds of the practitioner and the particular label or detection meansemployed. In some instances, the practitioner may first separatereaction products from one another using gel electrophoresis, asexemplified below. Other separation methods, i.e., chromatography, canalso be employed, but for some purposes, no separation will beperformed, and the detection of extended telomerase substrates and/orprimers will be carried out without removing the reaction mixture fromthe vessel in which the reaction was performed, as in a homogeneous PCRwhere one measures intercalation of a fluorophore in duplex DNA duringamplification. One important advantage of the present invention is theadaptability of the method to any detection format of interest.

The Multiplex Electrophoretic Separator (MES) is useful in analysis ofprimer extension products or any other samples with a mixture of targetnucleic acid and nonspecific dNTPs and/or primers (See Example 11) andis particularly useful for high throughput diagnostic assays. As shownin FIGS. 1A and 1B, the apparatus comprises a housing (1) containing areceptacle (2) adapted to receive a multiwell plate (3), and twoelectrodes (4). The electrodes are typically parallel to each other andpreferably movably attached to the housing to allow insertion of amultiwell plate onto the receptacle (2) that retains the multiwell platebetween the two electrodes, and have the same configuration as thesurfaces of the multiwell plate (i.e., the electrode covers the surfaceof all wells present in the microtiter plate in preferred embodiments).The multiwell plate typically has 24, 48, 96 or more wells per plate, insingle (i.e., a strip of microtiter wells) or multiple rows. Each well(5) is open at its upper surface (6) and has an open but sealable lowersurface (7), e.g., a Silent Monitor™ 96 well plate, Pall Corp., withremovable filter bottom, that can be resealed with adhesive tape. Themicrotiter plate is placed between two electrodes and connected to ameans for applying an electrical current, such as outlets for connectionto a power supply. The electrodes can be made of sheets of anyelectroconducting material, such as metallic sheets or wire metal grids(FIG. 1).

This apparatus can be used to separate a mixture of compounds inmultiple samples by preparing an electrophoretic matrix, such as apolyacrylamide or agarose gel, in a sealed well. The seal is removed,the plate is placed in the receptacle (2) above an electrode, and theelectrophoretic matrix is immersed in electrophoretic buffer.Alternatively, the buffer contacting the negative and positiveelectrodes can be provided in two chambers, where the only points ofcontact between the two chambers is through the electrophoretic matrix.The mixture to be separated is prepared for electrophoresis essentiallyas for conventional electrophoresis and then applied to the surface ofthe electrophoretic matrix. A second electrode is placed above themultiwell plate, and both electrodes are connected to a power supply,thus allowing separation of the components of the reaction mixture.Electrophoresis is continued until the non-incorporated dNTPs andprimers have eluted from the matrix, after which the gel is optionallyrinsed or washed and the products inside the matrix detected by anappropriate means for the label used. A combination of labels can beused in labelling primers so that different products (e.g., primerextension products of extended telomerase substrates and of a controlnucleic acid) can be detected in a single well.

Streptavidin-coated microtiter well-plates (Boehringer Mannheim) canalso be used for detection of amplified or non-amplified telomeraseextension products. One illustrative method involves labelling the 5'end of a telomerase substrate with biotin, capturing the extendedtelomerase substrates in the streptavidin-coated microtiter well-plates,and detecting the presence of extended telomerase products by a labelledprobe complementary to telomeric repeats. As noted above, the label canbe a radioisotope or a fluorescent, phosphorescent, chemiluminescent, orenzymatic molecule, or any of various chromophores, epitopes orantigens. Of course, the reverse of this procedure, where the extendedtelomerase substrates are captured by a biotinylated return primer(e.g., (CTR)₄, CX, ACT, ACX, LC) and detected by a probe complementaryto the extended telomerase substrate can also be used. The extendedproducts can also be captured by capture probes bound to the plates thatare complementary to the telomerase substrate or to telomeric repeats.

Extended products can also be captured by incorporating biotin-labelleddNTP (e.g., biotin-dUTP) during telomerase extension or productamplification and capturing the extended product in the streptavidinplate. The products are then detected by probe complementary to thetelomerase substrate or to telomeric repeats.

Applications

Having this description of the method and reagents employed, one canconsider applications for the telomerase assay of the present invention,which include research, diagnostic and other applications. Because theassay is fast, simple, and amenable to single reaction vessel reactions,the assay can be used in research and clinical laboratory settings wherethere is a need to detect telomerase-positive cells or samples. Suchapplications include, but are not limited to: (i) detection of immortalcells in tumor biopsies for the identification of potential cancercells, before or after therapy; (ii) identification in a cell-based orcell-free screen of agents capable of activating, derepressing,inhibiting, or repressing telomerase, including immortalizing agents(e.g., oncogenes) or compounds that activate telomerase and extendtelomeres and replicative lifespan of cells; (iii) identification inculture systems or in vivo of stem cells, early progenitor cells, orfetal cells that possess telomerase activity; (iv) examination oftelomerase regulation during differentiation and development; (v)identification of telomerase-positive fractions generated duringpurification of telomerase; (vi) identification of protozoal or fungalinfections; (vii) diagnosis of diseased states or medical conditionscharacterized by a different level of telomerase activity in a patientrelative to an individual not having the diseased state or particularmedical condition; and (viii) diagnosis of certain types of infertilitycharacterized by an absence of telomerase activity.

The diagnostic methods of the present invention can be employed with anycell or tissue type of any origin and can be used to detect an immortalcell of any origin, provided the cell expresses telomerase activity. Forhuman samples, the detection of immortal cells will typically be used todetect the presence of cancer cells of any of a wide variety of types,including without limitation, solid tumors and leukemias including:apudoma, choristoma, branchioma, malignant carcinoid syndrome, carcinoidheart disease, carcinoma (e.g., Walker, basal cell, basosquamous,Brown-Pearce, ductal, Ehrlich tumor, Krebs 2, merkel cell, mucinous,non-small cell lung, oat cell, papillary, scirrhous, bronchiolar,bronchogenic, squamous cell, and transitional cell carcinomas),histiocytic disorders, leukemia (e.g., B-cell, mixed-cell, null-cell,T-cell, T-cell chronic, HTLV-II associated, lymphocytic acute,lymphocytic chronic, mast-cell, and myeloid leukemias), histiocytosismalignant, Hodgkin's disease, immunoproliferative small, non-Hodgkin'slymphoma, plasmacytoma, reticuloendotheliosis, melanoma,chondroblastoma, chondroma, chondrosarcoma, fibroma, fibrosarcoma, giantcell tumors, histiocytoma, lipoma, liposarcoma, mesothelioma, myxoma,myxosarcoma, osteoma, osteosarcoma, Ewing's sarcoma, synovioma,adenofibroma, adenolymphoma, carcinosarcoma, chordoma,craniopharyngioma, dysgerminoma, hamartoma, mesenchymoma, mesonephroma,myosarcoma, ameloblastoma, cementoma, odontoma, teratoma, thymoma,trophoblastic tumor, adenocarcinoma, adenoma, cholangioma,cholesteatoma, cylindroma, cystadenocarcinoma, cystadenoma, granulosacell tumor, gynandroblastoma, hepatoma, hidradenoma, islet cell tumor,leydig cell tumor, papilloma, sertoli cell tumor, theca cell tumor,leiomyoma, leiomyosarcoma, myoblastoma, myoma, myosarcoma, rhabdomyoma,rhabdomyosarcoma, ependymoma, ganglioneuroma, glioma, medulloblastoma,meningioma, neurilemmoma, neuroblastoma, neuroepithelioma, neurofibroma,neuroma, paraganglioma, paraganglioma nonchromaffin, angiokeratoma,angiolymphoid hyperplasia with eosinophilia, angioma sclerosing,angiomatosis, glomangioma, hemangioendothelioma, hemangioma,hemangiopericytoma, hemangiosarcoma, lymphangioma, lymphangiomyoma,lymphangiosarcoma, pinealoma, carcinosarcoma, chondrosarcoma,cystosarcoma phyllodes, fibrosarcoma, hemangiosarcoma, leiomyosarcoma,leukosarcoma, liposarcoma, lymphangiosarcoma, myosarcoma, myxosarcoma,ovarian carcinoma, rhabdomyosarcoma, sarcoma (e.g., Ewing's,experimental, Kaposi's, and mast-cell), neoplasms (e.g., bone, breast,digestive system, colorectal, liver, pancreatic, pituitary, testicular,orbital, head and neck, central nervous system, acoustic, pelvic,respiratory tract, and urogenital), neurofibromatosis, and cervicaldysplasia.

In one aspect of the invention, telomerase activity is determined from abody fluid (e.g. urine, phlegm, sputum, saliva, blood), a fine needleaspirate or biopsy to diagnose cancer, such as urogenitory cancer,bladder cancer, lung cancer, and leukemia. Preferably, the cell sampleis obtained by using a non-invasive method to collect a fluid sample andthen isolating cells therefrom, for example, by centrifugation,filtration or other physical means. This simple method of obtainingcells for screening for different cancers is particularly suited to theclinical setting.

Telomerase activity can then be assayed, allowing for diagnosis based onthe presence of telomerase activity. In the diagnostic methods of theinvention, the assay will be conducted to determine whether an elevatedlevel of telomerase is present. The phrase "elevated level" means thatthe absolute level of telomerase activity in the particular cell iselevated compared to normal somatic cells in that individual, orcompared to normal somatic cells in other individuals not suffering froma disease condition. Generally, any detectable level of telomeraseactivity is considered elevated in cells from normal, postnatal humansomatic tissue. Although telomerase activity is present in germlinecells, and low levels of telomerase activity can be detected in stemcells and certain hematopoietic system cells, such cells do not presentproblems for the practitioner of the present method. Germline cells canbe readily distinguished and/or separated from human somatic tissuesamples, and the telomerase activity present in stem cells and certainhematopoietic cells is present at such low levels that the few suchcells present in somatic tissue samples will not create false positivesignals from a telomerase activity assay or can be detected anddistinguished using other means. The detection of telomerase activity insomatic cells is indicative of the presence of immortal cells, such ascertain types of cancer cells, and can be used to make thatdetermination even when the cells would be classified as non-cancerousby pathology. Thus, the method of the present invention allows cancerousconditions to be detected with increased confidence before cells becomevisibly cancerous.

The diagnostic tests of the invention can also be carried out inconjunction with other diagnostic tests. In some instances, suchcombination tests can provide useful information regarding theprogression of a disease, although the present method for testing fortelomerase activity provides much useful information in that regard aswell. When the present method is used to detect the presence of cancercells in a patient sample, the presence of telomerase activity can beused to determine where a patient is at in the course of progression ofthe disease, whether a particular tumor is likely to invade adjoiningtissue or metastasize to a distant location, and whether cancer islikely to recur or has recurred. Tests that may provide additionalinformation in conjunction with the present method include diagnostictests for DNA ploidy, fraction of cells in S-phase, nodal status,Her-2/neu gene products, p53, p16, p21, ras, and other oncogenes.

The level of telomerase activity can also be used to monitor theeffectiveness of chemotherapeutics during cancer treatment. The level oftelomerase can be a monitor of the effectiveness of a telomeraseinhibitor or retinoid therapy, or any other cancer therapy, wheretelomerase activity is decreased through telomerase inhibition, cellulardifferentiation, or cell death, respectively. The level of telomerasecan monitor the effectiveness of any oncolytic or tumor-debulkingprocedure by providing an estimate of the number of immortal cellswithin the patient.

Telomerase activity, or the presence of telomerase components, can alsobe determined as a marker for fetal cells, e.g., collected from cord ormaternal blood. Identification of fetal cells in maternal blood isuseful in diagnosing pregnancy or in the genetic testing of fetal cells,i.e., to identify the cells to be tested.

Telomerase activity can also be used as a marker for bone marrowproliferation. A bone marrow transplant is typically more successfulwhen less differentiated bone marrow cells are employed. Becausehematopoietic cells lose telomerase activity as they differentiate, thepresence of telomerase activity can be used as a marker forhematopoietic cells useful for transplant purposes. Any of the currentassays for telomerase activity, as well as assays that may be developedin the future can be used.

The present invention also provides kits for performing the diagnosticmethod of the invention. Such kits can be prepared from readilyavailable materials and reagents and can come in a variety ofembodiments. For example, such kits can comprise, in an amountsufficient for at least one assay, any one or more of the followingmaterials: oligonucleotide telomerase substrates (e.g., TS), controlreagents (e.g., control oligonucleotides (e.g., TSNT, TSR8), positivecontrol extracts or cell pellets), and oligonucleotide primers (e.g.,CX, ACT, ACX, LTS, CLT, LC, LG, NT), optionally provided together withany of the following: reaction vessels, buffers (e.g., cell lysisbuffer, end-labelling buffer, TRAP reaction buffer), water (preferablyRNase, DNase and protease-free), nucleotides, labels or stains (e.g.,SYBR Green, fluorescer, labelled oligonucleotide probes, such as bDNAprobes ), enzymes (e.g., RNA or DNA polymerase, ligase, RNase,polynucleotide kinase), other reagents necessary or helpful to performthe assay, and instructions. Typically, instructions include a tangibleexpression describing the reagent concentration or at least one assaymethod parameter, such as the relative amounts of reagent and sample tobe admixed, maintenance time periods for reagent/sample admixtures,temperature, buffer conditions, and the like, to allow the user to carryout any one of the assays described above.

In one embodiment of the invention, the kit comprises a reaction tube inwhich is placed a telomerase substrate and a primer. A preferred form ofthis kit comprises such a tube in which the primer is separated fromother reaction components by a wax barrier. The primer may be coated onor attached to a glass bead. A wide variety of kits and components canbe prepared according to the present invention, depending upon theintended user of the kit and the particular needs of the user. Otherformats utilize oligonucleotide primers, such as the ACX primer, thatallow wax-free assay conditions.

The reagents of any diagnostic assay described herein can be provided insolution, as a liquid dispersion or as a substantially dry power, e.g.,in lyophilized form, either independently or in a mixture of componentsto improve ease of use. Where an enzyme or other degradable reagent isprovided, conditions are chosen so as to stabilize the reagents, e.g.,storage at lower temperature, addition of stabilizing agents (e.g.,glycerol or a reducing agent). Unstable reagents can be providedtogether with or separately from the more stable components of the kit.A solid support such as a multiwell plate, glass beads, or tubes, andone or more buffers can also be included as separately packaged elementsin a kit. The kits discussed herein in relation to diagnostic methods orresearch applications are similar in a general sense to thosecustomarily utilized in diagnostic systems and so can include glass andplastic (e.g., polyethylene, polypropylene and polycarbonate) bottles,vials, plastic and plastic-foil laminated envelopes, and the like.

The following examples describe specific aspects of the invention toillustrate the invention and provide a description of the present methodfor those of skill in the art. The examples should not be construed aslimiting the invention, as the examples merely provide specificmethodology useful in understanding and practice of the invention.

EXAMPLE 1 Preparation of CHAPS-Extracted Telomerase

In this Example, cell extracts prepared using the zwitterionicdetergent-based extraction method of the invention were tested fortelomerase activity using the conventional telomerase assay.

The cell extracts were prepared from immortal 293 cells, which are knownto express telomerase activity and are derived from human embryonickidney cells transformed with fragments of adenovirus type 5 DNA. Thecells were grown in Joklik's medium containing 5% to 10% fetal bovineserum and then collected by centrifugation (unless otherwise noted, theprocedure below assumes that about 1×10⁶ cells were collected), washedonce in PBS, pelleted at 10,000×g for 1 minute at 4° C., and resuspendedin 1 ml of ice-cold PBS. The cells were pelleted again and resuspendedin ice-cold lysis buffer 10 mM Tris-HCl (pH 7.5), 1 mM MgCl₂, 1 mM EGTA,0.1 mM PMSF (benzamidine or AEBSF can also be used), 5 mMβ-mercaptoethanol, DEPC-treated water, 0.5% CHAPS (from Pierce), 10%glycerol! at a concentration of 20 μl of lysis buffer per 10⁴ -10⁶ cells(depending on the purpose of the experiment). The suspension wasincubated on ice for 30 minutes and then spun in a microultracentrifugeat 10,000×g for 30 minutes at 4° C. The supernatant was removed toanother tube, quick-frozen on dry ice, and optionally stored until useat -70° C. These extracts typically contained a total proteinconcentration of 5 to 10 mg/ml, and the telomerase activity was stableto multiple freeze-thaws.

The procedure for and conditions of the conventional telomerase assaywere as described by Counter et al., 1992; Counter et al., 1994, EMBO J.11:1921-1929; and Counter et al., 1994, J. Virol. 68:3410-3414, usingoligonucleotide substrates at a concentration of 1 μM. See also Morin,1989, Cell 59:521-529. The products were separated on an 8%polyacrylamide sequencing gel and exposed overnight to a Phosphorimager™screen (Molecular Dynamics, Sunnyvale, Calif.). The telomerasesubstrates used in the conventional assay were 5'-GTTAGGGTTAGGGTTAGG-3'(abbreviated as "(GTTAGG)₃ "; SEQ ID NO:15); 5'-TTAGGGTTAGGGTTAGGG-3'(abbreviated as "(TTAGGG)₃ "; SEQ ID NO:16), and5'-AATCCGTCGAGCAGAGTT-3' (abbreviated as "TS"; SEQ ID NO:3). Controlsamples were also assayed, which contained extracts pretreated withRNase by incubation of 10 μl of extract with 0.5 μg of RNase(DNase-free, Boehringer Mannheim) for 10 minutes at 25° C., whichdegrades the RNA component of telomerase and abolishes activity.Telomerase pauses after adding the first G of the G triplet, so thenumber of nucleotides added before the first pause (and thus the phasingof the ladder) is five for (GTTAGG)₃ (SEQ ID NO:15), four for (TTAGGG)₃(SEQ ID NO:16), and two for the TS oligonucleotide.

The results demonstrated that the CHAPS-extracted telomerase activityfunctioned as predicted for human telomerase. The detergent-extractedactivity produces a six nucleotide ladder of extension productscharacteristic of telomerase activity. A shift in product phase isobserved dependent upon the 3'-sequence of the oligonucleotidetelomerase substrate, as is expected for telomerase-mediated extension,and the extracted telomerase can extend a non-telomeric oligonucleotidepreviously shown to be a telomerase substrate (Morin, 1991, Nature353:454-456) with 5'-TTAGGG-3' repeats (as confirmed usingdideoxynucleotide chain termination sequencing). The activity wasabolished by RNase treatment, as would be expected for telomeraseactivity (Greider and Blackburn, 1985, Cell 43:405-413; Greider andBlackburn, 1989, Nature 337:331-337; Morin, 1989, Cell 59:521-529).

EXAMPLE 2 PCR Amplification of Telomerase Extension Products

This example illustrates the telomerase assay method of the presentinvention in which a DNA polymerase is used to mediate the primerextension reaction in a polymerase chain reaction. The reactioncomponents include the telomerase substrate TS (the sequence of which isprovided in Example 1, above), which telomerase extends by synthesizingtelomeric repeats and which also functions as the upstream primer in thePCR step, and the downstream primer CX, the structure of which is defmedby its sequence 5'-(CCCTTA)₃ CCCTAA-3' (SEQ ID NO:1). Mismatches weredesigned in the CX primer/extended telomerase substrate to reduceinteraction between the CX primer and unextended TS oligonucleotidetelomerase substrate and so minimize primer-dimer (more accurately CXprimer/TS dimer formation).

As noted above, telomerase is known to extend oligonucleotides ofnon-telomeric sequence, such as the TS oligonucleotide (Morin, 1991,Nature 353:454-456), and oligonucleotide substrate TS was used to avoidnon-specific amplification due to PCR primer complementarity. As furthermodifications to avoid primer interaction, mismatches (relative to TS)in the downstream primer CX, single stranded binding protein T4 gene 32protein, hot start PCR, and an annealing temperature of 50° C. were usedto conduct the telomerase activity assays described in this Example.Under these conditions, specific amplification occurs only if theoligonucleotide substrate has been extended with three or more5'-TTAGGG-3' repeats, resulting in a six nucleotide ladder of TRAP assayproducts extending from 40 nucleotides (the first amplifiable telomeraseproduct) up to the limit of gel resolution.

Yet another important modification that greatly improves the ease andefficiency of the present method relates to the development of a novelreaction buffer in which both telomerase and DNA polymerase canfunction. Use of this buffer allows one to employ a single tube set-upor format for the TRAP assay. This modification allows one to increasethe specificity of primer extension, because the CX primer is initiallyseparated from the rest of the reaction mix by a wax barrier, whichmelts only at the higher temperatures that mediate stringenthybridization conditions. The assay tubes were prepared by adding 2 μlof a 50 ng/μl suspension of CX primer (0.1 μg), which was spun to thebottom of the tube and evaporated until dry in a Speed-Vac™ centrifuge.

A trace amount of bromophenol blue was added to the CX primer suspensionto monitor possible leakage through the wax barrier prior to thermalcycling. While the addition of dye for this purpose is in no wayrequired for practice of the present invention, dye addition can be aconvenient method for monitoring the integrity of a manufacturingprocess. Tubes were then heated at 70° C., and 7-10 μl of molten wax(Ampliwax™, Perkin-Elmer) was pipetted into the bottom of the tube.After the wax was allowed to solidify at room temperature, the tubeswere stored at 4° C. Tubes were warmed to room temperature before use.No effect on assay performance was observed using prepared tubes storedat 4° C. for up to two months; the expected shelf-life of such tubes(and kits comprising the same) is expected to be at least a year.

Reactions were typically carried out by the addition of 50 μl of TRAPreaction solution above the wax barrier. The reaction solution contained20 mM Tris-HCl, pH 8.3, 1.5 mM MgCl₂, 63 mM KCl, 0.005% Tween 20, 1 mMEGTA, 50 mM each dNTP, 0.1 μg of TS oligonucleotide, 0.5 mM T4 gene 32protein, 0.1 mg/ml BSA, 2 Units of Taq DNA polymerase (optionally use 2Units of Taq treated with an equal volume of TaqStart™ antibody fromClontech to enforce hot start PCR), and 1-2 μl of a CHAPS cell extract.For radiolabelling of products, 0.2 to 0.4 μl of 10 μCi/μl ³² P-dGTPand/or ³² P-dCTP (3000 Ci/mmol) was added to the reaction. After 10minutes at 20° C. for extension of oligonucleotide TS by telomerase, thetubes were transferred to the thermal cycler (96 well Singleblock™system, Ericomp) for 27 cycles, each cycle comprising incubationtemperatures and periods of 94° C. for 30 seconds, 50° C. for 30seconds, and 72° C. for 30 seconds to 1.5 minutes The CX primer (0.1 μg)was liberated when the wax barrier melted at ˜70° C. Those of skill inthe art will recognize that the reaction times, temperatures, andbuffers described in this Example can vary, depending upon the needs ofthe practitioner, the particular substrates and primers employed, andthe source of the extract and DNA polymerase (see Example 4).

For instance, the telomerase extension reaction can be conducted attemperatures ranging from about 10° C. to about 42° C., depending uponthe source of the telomerase. The telomerase reaction time can varywidely, depending upon the number of primer extension steps employed,the amount of telomerase expected to be in the sample, and the timeavailable to the practitioner. Typically, the telomerase reaction timewill be between 5 and 60 minutes, but the time could be up to severalhours. In similar fashion, the PCR cycles can be composed of cycle timesand temperatures that vary widely. The simplest PCR cycle comprises aduplex nucleic acid denaturation step followed by a primer annealing andextension step. While denaturation is typically carried out by heatingthe reaction mixture, other methods, such as helicase treatment, can beused, and the heating method itself can be conducted at a wide range oftemperature for any amount of time sufficient to denature but not damagethe DNA. In similar fashion, the time and temperature of the primerannealing step depends to a great extent on the reaction buffer andprimer sequence, concentration, and composition, as well as thespecificity required by the practitioner, while the time and temperatureof the primer extension step depends greatly upon the type of DNApolymerase employed. Those of skill in the art will recognize andunderstand that the present invention is not limited by the times,temperatures, and variations in buffer and other reaction componentsthat can be employed in the method.

For analysis of the samples, one half of the reaction mixture wasanalyzed by electrophoresis in 0.5×TBE on 15% polyacrylamidenon-denaturing gels. Visualization of the products was by ethidiumbromide staining, silver staining, SYBR™ Green staining (MolecularProbes) autoradiography, or Phosphorimager™ analysis (MolecularDynamics, Sunnyvale, Calif.) of the gels. Control samples were assayed,using: a sample from which the TS oligonucleotide was omitted; a samplefrom which the cell extract was omitted; a TRAP assay sample of animmortal 293 cell extract; a sample of 293 extract pretreated byincubation for 10 minutes at 65° C. to heat-inactivate the telomerase; asample of 293 extract pretreated by incubation for 10 minutes with 0.5μg of RNase (DNase-free, Boehringer Mannheim) at 25° C. to destroy theRNA component of telomerase; a sample of phenol-extracted 293 extract(by mixing in an equal volume of a 1:1 phenol:chloroform mixture,vortexing for 30 seconds, centrifuging to separate the phases, andcollecting the aqueous phase); a sample of 293 extract pretreated withprotease by incubation of the extract (50 μl) with 5 μg of Bromelainprotease (Boehringer Mannheim) for 10 minutes at 37° C., removal of theBromelin protease by incubation with an equal volume of carrier-fixedα2-macroglobulin (Boehringer Mannheim) for 30 minutes at 25° C. withshaking and then centrifugation (to pellet theα2-macroglobulin/Bromelain complex) for 10 minutes at 10,000×g, andcollection of the supernatant for analysis; a normal fibroblast BJ cellextract, which should lack telomerase activity; and a cell extractenriched for telomerase by DEAE chromatography (Morin, 1991, Nature353:454-456).

The results of these multiple control experiments demonstrate that apositive signal in the TRAP (Telomerase Repeat Amplification Protocol)assay requires a ribonucleoprotein in an immortal cell extract capableof extending the TS oligonucleotide with two or more 5'-TTAGGG-3'repeats, validating the assay for specific detection of telomeraseactivity.

To examine more closely the sensitivity of the TRAP assay, another setof assays was conducted to test the limits of detergent extraction andTRAP detection under the conditions employed. For extraction ofdifferent numbers of cells, the volume of lysis buffer was kept constantat 100 μl. No activity was observed in an assay of about 10⁵ cellequivalents from an extract of 10⁷ normal fibroblast BJ cells, asindicated by the absence of the ladder of bands. Telomerase activity wasobserved in an assay of about 10⁴ cell equivalents from an extract of10⁶ immortal 293 cells, in an assay of about 10³ cell equivalents froman extract of 10⁵ 293 cells, and in an assay of about 10² cellequivalents from an extract of 10⁴ 293 cells. No activity was observedin an assay of about 10 cell equivalents from an extract of 10³ 293cells or in a control assay with lysis buffer only.

The limit of telomerase detection in 10² cells was confirmed by TRAPassays of serial dilutions of an extract from 10⁶ 293 cells. This limitis a function of the TRAP assay conditions employed and should beconsidered a practical limit under the given set of conditions ratherthan an absolute limit of the sensitivity of the current method. Example15 is an illustrative example describing the detection of telomeraseactivity in a single cell. Those of skill in the art will recognize thatother means of increasing the sensitivity of the assay are available.For instance, use of primers CTR3 (5'-CCCTAA-3')₃ (SEQ ID NO:17)! orCTR4 (5'-CCCTAA-3')₄ (SEQ ID NO:18)! instead of CX further increasessensitivity, although these primers are more likely to interact with theunextended TS primer. The limit of sensitivity was also analyzed bytitration of the synthetic telomerase product TS+4 (which containsoligonucleotide TS followed by four telomeric repeats). Dilutions ofTS+4 oligonucleotide were mixed with heat-treated (telomeraseinactivated) 293 extract and analyzed in TRAP assays. In this analysis,the assay gave a clear positive signal from 10⁶ molecules of TS+4. Inaddition, telomerase activity from mouse tissue (telomerase activity ispresent in somatic cells of mice) and cell extracts was detected by TRAPassay even though the mouse telomerase by conventional assay was shownto be mostly non-processive (i.e., adds only a single repeat; Prowse etal., 1993, Proc. Natl. Acad. Sci. USA 90:1493-1497), indicating that theTRAP assay is detecting very low levels of processive mouse telomeraseactivity that cannot be visualized by the conventional assay or mousetelomerase is more processive under TRAP conditions.

For the convenience of the practitioner, the following productinformation is provided. Reaction tubes were 0.2 ml Strip-ease™ tubesfrom Robbins Scientific (Sunnyvale, Calif.) and were autoclaved beforeuse. All oligodeoxyribonucleotides were Ultrapure grade (HPLC-purified)obtained from Keystone Laboratory (Menlo Park, Calif.) and weresuspended in DEPC-treated H₂ O or TE buffer (10 mM Tris.Cl, pH 7.6; 1 mMEDTA, pH 8.0) at a concentration of 1 mg/ml. Taq DNA polymerase, Tween20, and T4 gene 32 protein were purchased from Boehringer Mannheim.Radioisotopes were purchased from NEN-Dupont. The dNTPs were purchasedfrom Pharmacia and were aliquoted, stored at -20° C., and thawed (nomore than twice) before use. All other reaction components weremolecular biology grade and purchased from Sigma, except when otherwisenoted. Diethylpyrocarbonate (DEPC)-treated, de-ionized, sterile H₂ O wasused routinely.

EXAMPLE 3 Relative Sensitivity of TRAP and Conventional TelomeraseAssays--Assay of Telomerase Activity in Normal Somatic and ImmortalCells

This Example describes telomerase assays conducted on cell samples ofimmortal cell lines and normal somatic cell cultures from differenttissues and individuals. Adherent cell cultures, such as BJ cells, anormal somatic cell culture of human skin fibroblasts, were grown to 80%confluency prior to extract preparation. The assays (10⁵ cellequivalents per reaction) were conducted as described in Examples 1 and2, above, and the results of the assay are summarized in Table 1, below.Assays were performed on the same 10 cell extracts, which were preparedusing the CHAPS detergent lysis method (see Examples 1 and 2, above).

Control samples were assayed with extracts pretreated with RNase, whichshould eliminate any telomerase activity in the sample. The breastcarcinoma line MCF-7/ADR-RES, pancreatic carcinoma line AsPC-1,prostatic carcinoma line PC-3, melanoma line M14, normal foreskinfibroblast cell culture BJ, lung carcinoma line NCI-H23, normal stromalfibroblast cell culture 31YO, normal lung fibroblast cell cultureIMR-90, ovarian carcinoma line OVCAR-3, colon carcinoma line COLO205,and immortal kidney cell line 293 were assayed. For conventional assays,10⁶ cell equivalents were used per reaction.

Some immortal cell lines (293, MCF-7/ADR-RES, NCI-H23, OVCAR-3, COLO205,M14) showed activity in both assays, others (AsPC-1 and PC-3) showedactivity only in the TRAP assay, and the normal somatic cell cultures(BJ, IMR-90 and 31YO) showed no detectable activity by either assay.These results demonstrate that the TRAP method can detect telomeraseactivity in extracts that test negative by the conventional assay.

This survey was expanded to include a total of 74 immortal cell linesand 22 normal somatic cell cultures from 18 different tissues, and theresults are summarized in Table 1, below. Each dividing cell culture wasdetergent-extracted and tested for telomerase activity using the TRAPassay. The specific immortal cell lines and normal somatic cell culturesare listed by tissue of origin. Immortal cell lines and normal somaticcell cultures tested were: (1) Skin--melanoma (LOXIMVI, M14, Malme-3M,UACC-62), normal fibroblasts (GFS, S37b, Malme-3, BJ), normalkeratinocytes (primary foreskin); (2) Connective--Fibrosarcoma(HT-1080); (3) Adipose--liposarcoma (SW872); (4) Breast--adenocarcinoma(MCF7, MCF-7/ADR-RES, MDA-MB-231), ductal carcinoma (T 47 D,MDA-MB-435), carcinoma (MDA-MB-157, MDA-MB-175-VI, MDA-MB-436,MDA-MB-468, ZR-75-1, ZR-75-30, UACC-812, UACC-893, BT-20, BT-474,BT-483, BT-549, HS578T, SK-BR-3, SCC70, SCC38, SCC202), normalepithelial and stromal cells (HME: 15, 17, 31, 32, 35); (5)Lung--carcinoma (NCI-H522, NCI-H23, A549, EKVK, 1299, H146, H69,NCI-H460, H358, H182), SV40 T-antigen transformed (IDH4, SW26-IG,SW-26-C4), normal fetal fibroblasts (GFL, IMR-90, Wi38); (6)Stomach--gastric carcinoma (KATO-III); (7) Pancreas--ductal carcinoma(SU.86.86), adenocarcinoma (AsPC-1, Capan-1); (8) Ovary--carcinoma(OVCAR-3, OVCAR-5, IGROV-1), adenocarcinoma (OVCAR-8); (9)Cervix--carcinoma (HeLa S3, C-33 A, HT-3), normal primary epithelialcells; (10) Uterus--normal primary endometrial cells; (11)Kidney--carcinoma (A498, CAKI-1), Ad5-transformed embryonic kidney cells(293); (12) Bladder--carcinoma (5637), transitional cell carcinoma(T24), squamous carcinoma (SCaBER), normal fetal (FHs 738B1); (13)Colon--adenocarcinoma (COLO 205, SW-620, HCT-116); (14)Prostate--adenocarcinoma (PC-3, DU 145), SV40 transformed BPHfibroblasts (BPH-1), normal stromal fibroblasts (31YO), BPH fibroblasts(S52); (15) CNS--carcinoma (U251, SNB-75), glioblastoma (SF268); (16)Blood--leukemia (Molt4, HEL), T-cell leukemia (Jurkats), acutepromyelocytic leukemia (HL-60), chronic myelogenous leukemia (K-562),histiocytic lymphoma (U-937); (17) Retina--SV40 transformed pigmentedepithelium (AGO6096A); and (18) Joint: normal synovial fibroblast (HSF).

                  TABLE 1    ______________________________________    Telomerase Activity in Mortal and Immortal Cells                Cell Type     Telomerase Activity                (Tumor/Transformed/                              (# positive/    Tissue of Origin                Normal/)      # tested)    ______________________________________    Skin        Tumor         4/4                Normal        0/5    Connective  Tumor         1/1    Joint       Normal        0/1    Adipose     Tumor         1/1    Breast      Tumor         22/22                Normal        0/8    Lung        Tumor         10/10                Transformed   2/3                Normal        0/3    Stomach     Tumor         1/1    Pancreas    Tumor         3/3    Ovary       Tumor         4/4    Cervix      Tumor         3/3                Normal        0/1    Uterus      Normal        0/1    Kidney      Tumor         2/2                Transformed   1/1    Bladder     Tumor         3/3                Normal        0/1    Colon       Tumor         3/3    Prostate    Tumor         2/2                Transformed   0/1                Normal        0/2    CNS         Tumor         3/3    Retina      Transformed   1/1    Blood       Tumor         6/6    ______________________________________

None of the normal somatic cell cultures displayed detectable telomeraseactivity in the TRAP assay. Of the 74 immortal cell lines, 68 weretumor-derived lines and 6 were cell lines transformed with viraloncoproteins. All of the 68 tumor lines contained telomerase activity.Two of the six transformed lines tested negative for telomeraseactivity. If these two lines are immortal, then the lack of detectabletelomerase activity is unexpected. However, an investigation of telomerelength in these lines showed that the telomeres were longer than thoseof the normal somatic cells from which the lines were derived, which mayindicate that the cells experienced a transient burst of telomeraseactivity. If the telomerase activity is not reinitiated, then the cellswill not replicate indefinitely.

EXAMPLE 4 Standard Operating Procedure for Telomeric RepeatAmplification Protocol (TRAP)

This Example provides a step-by-step protocol for performing the TRAPassay of the invention, in five parts: (A) Work station set-up; (B)Precautions; (C) Micro-extraction; (D) Quantitative Assay; and (E)Analysis. The method described provides for a quantitative analysis ofthe activity, and while a number of recommendations are made, those ofskill will recognize that, depending on the conditions used and natureof the results desired, not all recommendations need be followed in allcircumstances.

(A) Work Station Set-up

An important factor in the set-up of the TRAP assay is the environmentwhere the initial reaction mixtures are made prior to the PCR step. Theideal environment is free of contaminating ribonucleases and PCRamplified DNA products, which can cause erroneous negative and positiveresults, respectively. A major source of PCR product (and RNase)contamination can be the person performing the experiment, who shouldmaintain high standards of personal hygiene and avoid generation ofaerosols of PCR products when opening or pipetting PCR products ordisposing of gel buffer after the electrophoresis of PCR products. Apositive air displacement hood, which blows in filtered air over thesample toward the investigator, is ideal. Separate solutions, pipettes,tubes, and tips should always be used and kept inside the hood. Workspace should be wiped with 10% bleach prior to set-up of the reaction,and the hood should be routinely UV-irradiated when not in use. Also,barrels of pipettes should be periodically soaked in 10% bleach, evenwhen aerosol-resistant tips are used. The investigator should weargloves and a disposable lab coat with elastic wrist straps; the lab coatshould be periodically changed.

A dedicated work area for setting up TRAP reaction can be prepared byplacing an acrylic shield of 45.7 cm (L)×30.5 cm (W)×61 cm (H) size fromVWR (cat. #56615-848) on a standard cubby-hole type desk. The top of thedesk is covered either by a board or heavy cloth, and the front isblocked by the shield. This arrangement creates dead-air space, wherethe contaminants are prevented from falling into the working area fromoutside and the samples are physically blocked from the investigator.All the solutions, pipettes, tips, and tubes are kept inside thestation, and the working area is routinely UV irradiated by a short-waveUV lamp mounted on the top of the station (Black Ray UV lamp, XX-15S,VWR cat #36575-059).

(B) Precautions

As noted above, and because the TRAP assay incorporates both PCRamplification and use of in vitro activity of a ribonucleoprotein(telomerase), there is a need for extreme caution to prevent PCR-productcontamination (DNA) and RNase contamination, both of which can bedetrimental to the assay. The following basic precautions can befollowed in all steps of the assay protocol, including the telomeraseextraction and PCR amplification steps, to avoid problems: (1) useDEPC-treated H₂ O for all solutions, or commercially available nucleasefree water (Sigma) and aliquot the solutions in small amounts beforeuse; (2) keep the assay solutions (PCR buffer, CHAPS extraction buffers,dNTPs, Taq polymerase, etc.) separate from other reagents in thelaboratory; (3) wear gloves; (4) use a dedicated set of pipettors forthe assay and aerosol-resistant tips (ARTs); and (5) do not analyze theamplified samples in the same area where the samples are prepared (i.e.,do not open PCR tubes after the PCR amplification on the same benchwhere the assay reagents and pipettes/tips are located; instead useother pipettors (optionally without ARTs) at a location away from thePCR bench).

(C) Micro-extraction

The material requirements for the lysis buffer used in themicro-extraction procedure are shown below.

    ______________________________________    Lysis Buffer (0.5% CHAPS or CHAPSO)    Stock        Final      0.5 mL     10 mL    ______________________________________    1M Tris-HCT pH 7.5                 10     mM      5     μl                                           100  μl    1M MgCl.sub.2                 1      mM      0.5   μl                                           10   μl    0.5M EGTA    1      mM      1     μl                                           20   μl    *0.1M benzamidine                 0.1    mM      0.5   μl                                           10   μl    *βME(14.4M)                 5      mM      0.17  μl                                           3.5  μl    10% (w/v) CHAPS or                 0.5%   (w/v)   25    μl                                           500  μl    CHAPSO Detergent    100% Glycerol                 10%    (v/v)   50    μl                                           1    ml    DEPC H.sub.2 O              417.83                                      μl                                           8.36 ml    ______________________________________     *0.1M benzamidine (1 μl) and betamercaptoethanol (0.35 μl) are adde     to 1 ml of lysis buffer just prior to performing the extraction step; PMS     or AEBSF can be used in place of benzamidine.

The micro-extraction procedure involves the following steps:

1. Establish cell number by counting or by extrapolation from tissueweight.

2. Pellet the cells or tissue, wash twice in PBS (Ca and Mg-free),repellet, and remove PBS. Cells or tissue can be stored at -80° C. atthis point.

3. Resuspend cell pellet in 200 μl of lysis buffer per 10⁶ -10⁵ cells(depending on the application). For tissues, 200 μl of lysis buffer isused for 20-100 mg of tissue. Tissues can be treated by any of thefollowing (a, b or c) methods.

a) Soft tissues are homogenized using a motorized disposable pestle (VWRcat. #KT749520-0000, KT749540-0000). Firstly, the tissue sample isminced with a sterile blade until a smooth consistency is reached. Thesample is transferred to a sterile 1.5 ml centrifuge tube and lysisbuffer is added. Then the sample is homogenized with a motorized pestleon ice (˜10 sec) until a uniform consistency is achieved.

b) Connective tissue is placed in a sterile mortar and frozen by theaddition of liquid nitrogen. The sample is then pulverized by grindingwith a matching pestle. The thawed sample is then transferred to asterile 1.5 ml centrifuge tube and resuspended in lysis buffer.

c) Connective tissue is mixed with lysis buffer and the mixture ishomogenized using a mechanical homogenizer (e.g., PowerGen™ Model 35Homogenizer, Fisher, cat #15-338-35H) on ice until uniform consistencyis achieved (˜5 sec). Homogenization of the sample on ice prevents thesample from heating up which would potentially destabilize proteins.

4. Incubate the cells or treated tissue on ice for 30 minutes.

5. Spin the cells or treated tissue in a microcentrifuge (Eppendorf) at12,000 g for 30 minutes at 4° C.

6. Remove extract to another tube and use 1 to 2 μl per TRAP assay; onecan quick-freeze the remainder on dry-ice and store at -70° C., ifdesired. Typical protein concentrations are between 1 and 10 μl.

(D) Quantitative Assay

The following materials are recommended for the assay: TS primer(5'-AATCCGTCGAGCAGAGTT-3'; SEQ ID NO:3; HPLC purified, 1 μl); ACX primer(5'-GCGCGG CTTACC!₃ CTAACC-3'; SEQ ID NO:4; HPLC purified, 0.1 μl); NTprimer (5'-ATCGCTTCTCGGCCTTTT-3'; SEQ ID NO:6; HBPLC purified, 0.1 μl);TSNT internal control (5'-AATCCGTCGAGCAGAGTTAAAAGGCCGAGAAGCGAT-3'; SEQID NO:5; HPLC purified, 0.01 amol/μl); TSR8 quantitation standard(5'-AATCCGTCGAGCAGAGTTAG GGTTAG!₇ -3'; SEQ ID NO:19; HPLC purified, 1amol/μl); 2.5 mM dNTPs (Pharmacia); Taq DNA polymerase (Perkin Elmer;AmpliTaq™); and 10×TRAP Buffer.

    ______________________________________    10X TRAP Buffer    Components      For 5 ml    ______________________________________    200 mM Tris-HCl, pH 8.3                    1 ml (1M Tris-Cl pH 8.3)    15 mM MgCl2     75 μl (1M MgCl.sub.2)    630 mM KCl      3.15 ml (1M KCl)    0.5% Tween 20   250 μl (10%, Boehringer Mannheim)    10 mM EGTA      250 μl (0.2M EGTA)    1 mg/ml BSA     250 μl (20 mg/ml)                    (Boehringer Mannheim, Fraction V)    water (protease, RNase, and                    25 μl    DNase-free)    ______________________________________

For a quantitative assay, one can use an end-labelled TS substrate, inwhich case, the substrate/primer can be end-labelled with ³² P!γATPusing the reaction mixture described below, or with other reagents, suchas 5'-biotin, digoxigenin, fluorescein or another fluorophore, dependingon the particular detection and quantitation system to be employed:

    ______________________________________    End-Labelling Reaction Mixture    ______________________________________     .sup.32 P!γATP (3000 Ci/mmol, 10 μCi/μl)                           2.5 μl    TS primer (1 μg/μl)                           1.0 μl    10 x OPA buffer (Pharmacia)                           1.0 μl    T4 polynucleotide kinase (9.7 U/μl)                           0.5 μl    DEPC water             5.0 μl    ______________________________________

The end-labelling reagents are combined in a reaction vessel andincubated for 20 minutes at 37° C., followed by 5 minutes at 95° C. Itwill be apparent to the artisan that the end-labelling conditions (suchas amount of radioactive nucleotide or oligonucleotide) can be varieddepending on the particular application and needs of the practitioner.For example, increased sensitivity of the assay can be achieved byincreasing the specific activity of the labelled primer, as described inExample 15.

To prepare a telomerase assay reaction mixture, the following materialsare mixed in a PCR reaction tube.

    ______________________________________                          For 50 μl    Material              Total Volume    ______________________________________    10X TRAP Buffer       5       μl    2.5 mM dNTPs (Pharmacia)                          1       μl    End-labelled primer (0.1 μg/μl TS)                          1       μl    ACX primer (0.1 μg/μl)                          1       μl    NT primer (0.1 μg/μl)                          1       μl    TSNT internal control (0.01 amol/μl)                          1       μl    Taq polymerase (AmpliTaq ™ , Perkin Elmer)                          0.4     μl (2 Units)    DEPC treated H.sub.2 O                          37.6    μl    Telomerase Extract    2       μl    ______________________________________

Optional components include 0.2 μl of T4 gene 32 protein (5 mg/ml,available from Boehringer Mannheim), and 0.4 μl of TaqStart™ antibody(available from Clontech; the polymerase is mixed with the antibodyprior to the assay).

Controls

In the above reaction mixture, the telomerase extract can be replacedwith one of the following: a negative control RNase-inactivated orheat-inactivated extract (extract is heat-inactivated by incubation at75° C.-85° C. for 10 minutes); positive control cell extract; CHAPSlysis buffer (primer-dimer/PCR contamination control); and TSR8 (0.1amol quantitation control).

The reaction is carried out according to the following steps:

1. Incubate the reaction mixture at 30° C. for 10 minutes (this step canbe performed in the same instrument used to perform step 2);

2. Incubate the reaction mixture at the following temperatures for thetimes indicated to conduct the PCR: 94° C. for 30 seconds, then 60° C.for 30 seconds; repeat for 25-30 cycles;

3. Add loading dye containing bromophenol blue and xylene cyanol (0.25%each in 50% glycerol/50 mM EDTA), and subject samples to 10-15%,preferably 12.5%, nondenaturing PAGE in 0.5×TBE, until the bromophenolblue runs off the gel (molecular marker V from Boehringer Mannheim is agood DNA marker for this gel); and

4. Visualize product formation, e.g., by Phosphorimager™ screen (for aradioactive label) or another appropriate means of detection.

The presence of the TSNT internal control results in a specific PCRamplification product that appears as a band on a gel 14 bp below thefirst products of the TRAP assay, regardless of RNase treatment or noextract control. The internal control band can be used to normalize thePCR amplifications from different samples, and to calculate the numberof telomerase products generated when used in combination withend-labelled TS oligonucleotide substrate/primer as described below.

(E) analysis

i) Measure the signal of the region of the gel lane corresponding to theTRAP product ladder bands from all samples including non-heat-treated(x) and heat-treated sample extracts (x_(o)), CHAPS lysis buffer onlycontrol (r_(o)), and TSR8 quantitation control (r);

ii) Measure the signal from the TSNT internal standard innon-heat-treated samples (c) and TSR8 quantitation control (c_(R)).

iii) Quantitate the amount of telomerase product using the followingformula: ##EQU1##

Each unit of TPG (Total Product Generated) corresponds to the numbers ofTS primers (in 1×10⁻³ amole or 600 molecules) extended with at least 3or 4 or more telomeric repeats by telomerase in the extract. Typically,the assay has a linear range of 1 to 1000 TPG, which is equivalent totelomerase activity from approximately 10 to 10,000 control cells in a10 minute incubation at 30° C.

This calculation is valid only if the TS substrate is end-labelled anddoes not apply to a TRAP protocol in which direct incorporation ofradioactive dNTPs or non-radioactive quantitation is used for detection,because the signal would depend on the length of the products in thatcase. The primers should be present in excess over templates for thequantitative analysis to be accurate. Therefore, if a sample has veryhigh levels of telomerase activity, one can dilute the extract so thatthe PCR primers are not limiting.

Alternatively, one can add a control nucleic acid of any sequence to thereaction mixture in known amounts and amplify the control with primersdifferent from those used to amplify the extended telomerase substrate.The control oligonucleotide and/or the primers used to amplify thecontrol oligonucleotide can be labelled identically to or differentlyfrom the label used to label the telomerase extension products.

EXAMPLE 5 In Situ Detection of Telomerase Activity

This example illustrates the telomerase assay method of the presentinvention when applied in situ. The method involves internalization of atelomerase substrate by cells and detection of the extended telomerasesubstrate if telomerase is present in the cells. Those of skill in theart will recognize that numerous methods are available forinternalization of nucleic acids by cells and, in light of the presentspecification, a variety of methods can be used for the detection ofextended telomerase substrate. There is no limitation as to whichtelomerase substrate is used other than that imparted by the particulardetection method used. In one embodiment, a plasmid telomerase substrateis used. A preferred plasmid telomerase substrate is a selectable,multi-copy vector having a mammalian origin of replication, which vectorcomprises a non-telomeric telomerase substrate sequence (e.g., TSsequence, 5'-AATCCGTCGAGCAGAGTT-3') (SEQ ID NO:3) adjacent to arestriction site (e.g., Isce I) that is not present in the mammaliangenome. In this embodiment, the restriction endonuclease specific forthe restriction site is supplied to provide a linearized telomerasesubstrate. For example, a second plasmid containing the gene coding forthe specific restriction enzyme (e.g., Isce I), operably linked to aninducible promoter, is coinfected with the first plasmid into the targetcells. Upon induction, the plasmid encoding the unique restrictionenzyme expresses the restriction enzyme that cleaves the specificrestriction site present on the insert of the telomerase substrateplasmid. This results in a linearized telomerase substrate plasmid thatcan be elongated with TTAGGG repeats by telomerase.

A. Internalization of DNA substrate

Internalization of the substrates can be achieved using passiveinternalization (e.g., target oligonucleotides or DNA added to the cellmedia at a concentration of 10-100 μM), microporation by a detergent orStaphylococcus alpha toxins (BRL, following the manufacturer'sconditions), liposomes (e.g., LipofectAmine™, Lipofectin™, LipofectAce™,from BRL, following the manufacturer's conditions), or electroporation(e.g., in DMEM media with total volume of 0.8 ml, V=0.25 KV,Capacitance=960 μF, with no resistance in a electroporation cuvette with0.4 cm gap). After the target nucleic acid is internalized by the cells,the cells are incubated at 37° C. for 1-6 hours. For solid tissuesamples, frozen non-fixed tissue is cut into a thin section on acryostat, placed on a clean sterile microscopic glass slide andincubated at 37° C. with media containing DNA telomerase substrate, orDNA telomerase substrate incorporated into liposomes, for 1-6 hours.After the incubation, the tissue is gently washed with PBS, and fixedusing the methods discussed below. If active telomerase is present, theDNA substrate will be extended with de novo synthesis of TTAGGG repeats.

B. Sample fixation and permeabilization

After substrate internalization and incubation, the cells or sectionedtissues are treated to stop the telomerase reaction and any degradativeprocess and permeabilized to allow for detection. For example, thesamples can be washed or rinsed twice with PBS and fixed by any ofvarious methods known in the art, such as with MeOH:Acetic acid (3:1ratio, incubated overnight at -20° C.), with buffered 10% formalin (4-15hr at room temperature), with 3% paraformaldehyde (4-15 hr at roomtemperature), with 4% formaldehyde (4-15 hr at room temperature), orwith a commercially available fixative such as Permeafix (ORTHO, 1-5 hrat room temperature) can be used. The cells are then fixed onto amicroscopic glass slide by Cytospin™ (Shandon) and dried overnight atroom temperature. The fixed samples are then permeabilized by a proteasetreatment (e.g., proteinase K, pronase, trypsin, pepsin 2 mg/ml!) for10-60 minutes at room temperature. The samples can then be washed orrinsed with PBS at room temperature for 10 min, washed briefly with 100%EtOH, and air dried.

C. Detection of extended telomerase

After permeabilization of the samples, the extended telomerasesubstrate, if present, can be detected by various means. In one aspectof the present invention, PCR detection is used. Various in situ PCRconditions using illustrative TS and CTR5 primers ( 5'-CCCTAA-3'!₅, SEQID NO:20) are described below. Other primer pairs and reactionconditions can be utilized as is apparent to one of skill in the art.With the GeneAmp™ in situ PCR system 1000 and GeneAmp™ in situ PCR corekit (Perkin Elmer), 50 μl of reaction mix (10 mM Tris-HCl, 50 mM KCl, pH8.3; 2.5 mM MgCl₂ ; 200 μM dNTPs; 1 μM TS and CTR5 primers; 10 UAmpliTaq™ DNA polymerase) is added to the sample heated to 70° C.,sealed with a silicone gasket and clip (following the manufacturer'sprotocol, Perkin Elmer), and amplified for 30 cycles of 94° C./40 sec,55° C./90 seconds. For direct detection of the amplified products,tagged dUTP or primers (tagged by fluorescent labels, radioisotope,biotin or digoxigenin, with a ratio of tagged dUTP to dTTP of 94 μMT-dUTP:106 μM dTTP) can be incorporated during the PCR amplification.After completion of the last PCR step, the sample is washed 3 times inwash buffer (4×SSC; 0.05% Tween 20) at 70° C., for 2 minutes.

To reduce background signals that can arise from direct incorporation oftagged dNTPs into cellular DNAs, prior to the in situ PCR amplification,samples can be pretreated with dNTPs and a DNA polymerase without theprimers, optionally with a DNA ligase. The DNA polymerase, preferablyTaq DNA polymerase, forms a complementary copy of any single-strandedregions in the cellular DNA and the ligase, preferably a thermostableligase, eliminates any nicks in the resulting product. The addition ofDNA polymerase in the amplification step is thus not required if thesample is pretreated with a thermostable DNA polymerase.

D. Signal detection

Fluorescent in situ hybridization (FISH) can be employed to identifytelomerase positive cells in a mixed population of cells or tissues.After permeabilization of a tissue or cell sample fixed onto amicroscopic glass slide, the nucleic acids are denatured by immersingthe slide in 70% deionized formamide/2×SSC solution pre-warmed to70°-74° C. for 2-3 minutes. The slide is transferred to ice-cold 70%EtOH, and then to 95% EtOH, and then to 100% EtOH (4 minutes in eachsolution). Labelled probe (e.g., 100-200 ng of a plasmid insertcontaining about 500 bp of 5'-TTAGGG-3' repeat sequence is used perslide. The probe can be labelled with biotin, digoxigenin, radioisotope,or a fluorescent tag. After labelling, the probe is dried, resuspendedin 10 μl of 100% deionized formamide, denatured by incubation at 75° C.for 8 minutes, and immediately cooled on ice. To this, 10 μl of2×hybridization buffer (4×SSC; 4×Denhardt's solution; 20% dextransulfate; 100 mM Tris, pH 7.5) is added. The probe/hybridization mix (20μl) is added to the fixed sample, overlayed with a coverslip, and thecoverslip sealed with rubber cement or nail polish before incubating thesample at 37° C. for 8-48 hours. The coverslip is then removed and thesample is washed twice with 2×SSC/50% deionized formamide at 37° C., andthen twice with 2×SSC at 37° C. (5 minutes per wash).

If the DNA probe is labelled with a fluorescent tag or radioisotope, thesample can be mounted in antifade solution (VectaShield™, VectaLab), ordeveloped using a photographic emulsion, and viewed under a microscope.Digoxigenin-labelled probes are detected following the manufacturer'sconditions using conjugated anti-digoxigenin antibodies (BoehringerMannheim). If the probe is labelled with biotin, the slide can beblocked with 2×SSC/1% BSA for 10 minutes at room temperature, and thenincubated in fluorescent conjugated avidin/2×SSC/1% BSA (final avidinconcentration: 5 μg/ml) at room temperature for 1 hour. The slide canthen be washed 5 minutes at room temperature in the following series:4×SSC, 4×SSC/0.1% Triton X-100, 4×SSC, PN buffer (0.1M Na₂ HPO₄ ; 0.1MNaH₂ PO₄ and 0.1% Nonidet P40). The sample can be mounted in antifadeand viewed under a microscope. For amplification of the signal, theslide is blocked in PNM buffer (PN buffer plus 5% w/v! non-fat driedmilk) at room temperature for 10 minutes, and incubated in a solution ofbiotinylated anti-avidin antibody (5 μg/ml) in PNM buffer at roomtemperature for 20 minutes. The slide is then washed in the four-stepwash series described above, blocked again with PNM buffer, andincubated with fluorescently conjugated avidin (5 μg/ml) in PNM bufferat room temperature for 20 minutes. The slide is washed again by thefour-step wash series, mounted in antifade and the result is viewedunder a microscope.

It will be apparent to one of skill in the art that many variations ofthe in situ hybridization protocol described above can be applied in themethods of the invention. For example, a variation to the above in situhybridization detection method involves primed-in situ labelling (PRINS;Koch, J., in "Nonradioactive in situ Hybridization Application Manual"(1992), Boehringer Mannheim, 31-33). Detection of telomere repeats byPRINS involves using an oligonucleotide probe specific for telomererepeats and chain elongation incorporating labelled nucleotides.

PRINS mixture (10 μl) of 5% (v/v) glycerol; 10 mM Tris-HCl, pH 8.3; 100mM KCl; 0.05% (w/v) Tween 20; 0.75 mM EGTA; 2.5 mM MgCl₂ ; 0.4 μM returnprimer e.g., CTR₄ !; 200 μM dATP, dGTP, dCTP; 110 μM dTTP; and 90 μMlabelled dUTP, is placed on the fixed, permeabilized sample, sealed witha coverslip, anchored with nail polish, overlayed with mineral oil, andincubated at 70° C. for 30 minutes to 3 hours. After completion of thePCR, the sample is washed 3 times in wash buffer (4×SSC; 0.05% Tween 20)heated to 70° C. for 2 minutes and the signal can be observed asdescribed above.

To reduce the background signals that can arise from directincorporation of fluorescent tags during the PCR amplification, indirectdetection that involves PCR amplification using non-tagged dNTPs andunlabelled primers is used. In situ hybridization is then utilized todetect the PCR amplified product using a product-specific taggedhybridization probe as described above.

E. Elongation of in situ PCR product

In situ PCR can be improved by minimizing leakage of PCR amplifiedproducts from the cell. For this reason, the PCR product is typicallylarger than 200 bp, preferably larger than 500 bp, and more preferablylarger than 700 bp. Alternatively, leakage of PCR products smaller than200 bp from the cellular matrix can be prevented by incorporation of"bulky" dNTPs (e.g., a biotin-labelled dNTP, a fluorescent-labelled dNTPor a digoxigenin-labelled dUTP) into the PCR product or by incorporationof a product extension primer into the in situ PCR protocol.Illustrative primers for such a protocol are a primer that containsmultiple copies (three to four) of a 6 bp repetitive incomplete (ormismatched) telomeric sequence (e.g., 5'-TTTCCC-3'!₃₋₄) (SEQ ID NO:21and SEQ ID NO:22) at its 5' end, followed by a sequence that is specificfor the target, an appropriate return primer, and a third primer thatcontains incomplete repetitive sequences (e.g., 5'-TTTCCC-3'!₄) (SEQ IDNO:22). These primers can be used to amplify the specific target by insitu PCR. The presence of the third primer elongates the PCR product dueto its staggered-binding to the 3'-end of the target PCR product. Theelongation of the PCR products can be further induced by decreasing theannealing temperature during the initial PCR condition.

For example, if the annealing temperature of the first primer to thetarget sequence is 60° C., the sample is initially amplified for 15-20cycles of 94° C./45 seconds and 60° C./45 seconds, then amplified for15-20 cycles of 94° C./45 seconds and 50° C./45 seconds. The loweredannealing temperature in the second PCR step favors staggered-binding ofthe third primer to the repetitive sequences and thus the generation ofelongated PCR products. The resulting elongated PCR products are lessprone to leakage through the cellular matrix, thus resulting in improvedsignal retention in in situ PCR analysis.

EXAMPLE 6 Preparation of TRAP Reaction Beads

This Example illustrates the use of a wax barrier to separate the PCRreturn primer from other reagents to ensure that the return primer isaccessible to the DNA polymerase, and any extended telomerasesubstrates, during the TRAP assay only at temperatures that ensurehighly specific nucleic-acid base pairing and so reduces nonspecificprimer extension and primer-dimer formation.

A primer solution (e.g., ACT; 5-10 ng/μg) with a trace amount ofbromophenol blue is mixed with clean sterile glass beads (e.g., ˜300micron in diameter, acid-washed, commercially available from Sigma). Thebromophenol blue can be added to monitor possible leakage through thewax barrier prior to thermal cycling. While the addition of dye for thispurpose is in no way required for practice of the present invention, dyeaddition can be a convenient method for monitoring the integrity of amanufacturing process. The mix is dried until the beads are coated withan appropriate amount of dried primers (See Example 2), and theprimer-coated beads are then mixed with hot molten wax. While vigorouslymixing, the bead/wax mixture is dispensed onto a clean surface bypipetting and then allowed to solidify. One bead droplet is added to aPCR tube and used in a TRAP assay using the conditions described inExample 2.

Alternatively, the primer solution (e.g., ACT; 5-10 ng/μl) is mixed withglass beads (˜1000 micron in diameter). An aliquot of hot molten wax (˜5μl) is placed into a plug mold having a covered lower surface and isleft to harden. The bead is placed on top of the hardened wax layer anda second aliquot of hot molten wax (˜5 μl) is placed into the mold overthe bead, and allowed to harden. The cover of the lower surface isremoved and the finished plug is pushed through the mold. One plug perTRAP assay is used instead of the conventional reaction tube, and theTRAP assay is conducted as described above in Example 2.

It will be apparent to those of skill in the art that many variations ofthese two embodiments are possible, such as the use of various primersand surfaces other than glass beads.

EXAMPLE 7 Wax-Free/Hot-Start-Free TRAP Assay

There are various formats for reducing primer-dimer artifacts other thanthe use of a wax barrier illustrated in Example 6, such as choice ofreaction conditions. For example, and without limitation, the additionof about 5% dimethylsulfoxide (DMSO) to the TRAP buffer can reduce theformation of primer-dimer artifacts. The addition of glycerol incombination with DMSO compensates for the potential enzymedestabilization caused by DMSO. Thus, addition of about 5% glycerol tosamples in TRAP buffer containing about 5% DMSO can be beneficial whereenzyme stability is critical.

Appropriate primer design can also be employed to reduce primer-dimerformation. An illustrative primer is the ACX return primer (5'-GCGCGGCTTACC!₃ CTAACC-3', SEQ ID NO:4) which is a chimeric oligonucleotidethat has the anchor sequence of the ACT primer (5'-GCGCGG-3') (SEQ IDNO:2) at its 5' end followed by a CX primer-based sequence that containsmismatches (5'- CTTACC!₃ CTAACC-3', SEQ ID NO:23) in 3 of 4complementary telomeric repeats (5'-TAACCC-3'). TRAP assays wereperformed essentially as described in Example 2 using 293 extracts witheither TS and ACX, or TS and ACT, in the presence of about 5% DMSO,using cold start conditions (i.e., without a wax barrier) and theproducts were separated on a 15% polyacrylamide gel. Control sampleslacked input extract, and one set of control samples included asynthetic telomerase product (TSR8; 5'-AATCCGTCGAGCAGAGTTAG CGGTTAG!₇-3' SEQ ID NO:19). Results with no input 293 extract or with syntheticproduct showed that the TS and ACT combination resulted in primer-dimerartifacts, whereas no primer-dimer artifacts were observed with TS andACX primers.

To test the robustness of the ACX primer, an attempt was made to induceprimer-dimer artifact formation with TS primer by incubating the TRAPassay mixture including TS and ACX on ice without a wax-barrier, andthen initiating a PCR amplification in a non-preheated thermocyclerblock. The combination of TS and ACX primers consistently showed noprimer-dimer artifact formations and had no detrimental effect on theefficiency of the TRAP reaction. Furthermore, TS and ACX primers wereequally resistant to primer-dimer formation in the absence of DMSO.Therefore, the utilization of the TS and ACX primers in the TRAP assaycan replace the wax-barrier methodology for the TRAP assay, thus makingthe analysis, manufacturing, and the performance of the TRAP assaycomponents more reproducible, simple, and reliable. However, as will beapparent to the artisan, such primers can be used in variousembodiments, including the wax-barrier methodology.

EXAMPLE 8 TRAP Product Detection by TaqMan™ Detection System

The method involves detecting extended telomerase substrates using thenon-radioactive TaqMan™ detection system (Perkin Elmer) modified for usein the TRAP assay. A TaqMan™ probe that possesses both a fluorescentreporter dye tag and a quencher dye tag is incorporated into the primerextension reaction (e.g., PCR amplification). Although there is noprecise limitations on the positions of these tags, it will be apparentto one of ordinary skill in the art that particular positions may bepreferable to others; for example, the tags are preferably positioned6-8 nucleotides apart.

An illustrative probe for use in this detection system comprisesrepetitive CTR (5'-CCCTAA-3') sequences. In a convenient format, the CTRprobe and return primer (e.g., ACT) are both separated by a wax barrierfor use in the hot-start methodology described in Example 2.

A second illustrative probe that comprises a sequence complementary tothe telomerase substrate does not compete with either the TS or ACTprimers, and thus does not result in primer-dimer formation. Althoughthe artisan may be concerned that the formation of a duplex between sucha probe with the TS primer can potentially decrease PCR efficiency,telomerase was demonstrated to recognize and extend such double-strandedsubstrates in an assay using PCR detection as described below.

A duplex DNA (GTSI-1) was constructed by hybridizing an equal amount ofM2A telomerase substrate primer (modified TS:5'-GCCCAATCCGTCGAGCAGAGTTAG-3'; SEQ ID NO:25) with its complementarysequence CM2A (5'-CTAACTCTGCTCGACGGATTGGGC-3'; SEQ ID NO:26). GTSI-1 wasused in a TRAP assay with the return primer, HKC (a variation of theanchored CTR primer: 5'-CTCGGTACCAAGCTTCTAACCCTAACCCTAACC-3'; SEQ IDNO:27), and 293 extract, under cold-start conditions (i.e., no waxbarrier) essentially as described in Example 2. The TRAP product wasobserved with this primer combination and was demonstrated to be RNasesensitive thus demonstrating the utility of probes that arecomplementary to the telomerase substrate in detecting telomeraseactivity. Thus, CM2A can be used as a TaqMan™ probe.

Modifications to the probe design are easily accomplished by those ofordinary skill in the art. For example, a probe can be used whichcontains a sequence complementary to the 3' region of the TS primer,followed by a CTR sequence (e.g., 5'-AACCCTAACCCTAACTCTGCT-3'; SEQ IDNO:7) with a reporter dye at is 5' end and a quencher dye internal tothe 5' end, preferably about 7 nucleotides internal to the 5' end. Thisprimer specifically hybridizes to the junction between the TS primer andthe telomeric repeat sequence thereby reducing any competitive effectthat may occur with the ACT-probe and TS-probe duplex formation. A probecontaining the TS sequence and at least one TTAGGG repeat can also beused in the TaqMan™ detection system, preferably using the hot startmethodology of Example 2.

EXAMPLE 9 Multiplex Electrophoretic Separator (MES)

The Multiplex Electrophoretic Separator (MES) is an apparatus thatallows for analysis of multiple samples simultaneously. The apparatuscomprises two electroconducting sheets (e.g., copper) with the sameconfiguration as a multiwell plate. The two sheets act as electrodes(FIG. 1). A 15% non-denaturing polyacrylamide gel was prepared in abottomless multiwell plate temporarily sealed to allow polymerization ofthe gel. After removal of the seal, the multiplex gel unit was placedequidistant from the two electrodes, and the complete apparatus wassubmerged in electrophoresis buffer (e.g., 0.5×TBE; 0.045M Tris-borate,0.001M EDTA).

For illustration of a method using the apparatus, radioactively labelledTS primer was used as a substrate in a TRAP assay using 10-fold serialdilutions of 293 cell extracts (from 10⁵ -10¹ cell equivalents)essentially as described in Example 2. As controls, 5-fold serialdilutions of the synthetic product TSR8 from 10 fmol-16 amol (seeExample 7) were also included. Each assay/dilution was prepared intriplicate.

After the TRAP reaction, each sample was loaded onto the top of a wellof the MES and an electric field was applied across the gel. Afterseparation of the products from non-incorporated dNTPs and primers, thegel was washed with water and the product inside the gel detected bymeans of a PHOSPHORIMAGER™ apparatus (Molecular Dynamics). In thisillustrative embodiment, a commercially available microtiter plate wasused. As the plate material had not been optimized for the assay,scattering of the radioactivity by the plastic walls of the MES gel unitcaused a haziness in the signal. However, this apparatus can be used todistinguish negative samples (RNase controls and no extract) frompositive samples, and telomerase activity could be detected in samplesdiluted 10000-fold with linear quantitation over an extensive range, upto 1000-fold under the selected reaction conditions. As is apparent tothe artisan, various materials can be used in the MES, and assayconditions can be varied in accordance with this specification.

EXAMPLE 10 Detection of Telomerase Activity with TRAP-SYBR Green

The TRAP assay is carried out on telomerase samples essentially asdescribed above in Example 4, typically in a total volume of 50 μl, butusing unlabelled primer. Typically, PCR parameters for the TRAP-SYBRGreen assay are 22-35 cycles of a two step program, i.e., 94° C./30seconds and 60° C./30 seconds. After electrophoresis, the gel is stainedwith SYBR Green to visualize products.

In an alternative embodiment, to reduce background, the reaction mixtureis treated with 25 μl of 0.3M acetate buffer, pH 4.5 containing 500 ngRNase and 10 units of S1 nuclease and incubated at 37° C. for 15 minutesto digest excess primers and RNA in the telomerase extract. As analternative to electrophoresis, aliquots (50 μl) of a 1:2000 dilution ofSYBR Green dye (Molecular Probes) can be added to wells of a microtiterplate, and 50 μl aliquots of the digested TRAP assay are mixed with thedye for measurement of telomerase activity. The double-stranded DNA/dyecomplex is detected with a fluorometric plate reader using an excitationwavelength of 497 nm and an emission wavelength of 520 nm. Such anon-radioactive telomerase assay is simple, inexpensive and, if desired,has the potential for high through-put screening in a clinical referencelaboratory or for screening compounds for telomerase inhibitoryactivity, and still allows easy quantitation of DNA products in asample.

EXAMPLE 11 Single-cell Telomerase Repeat Amplification Protocol (STRAP)

To illustrate the sensitivity of the TRAP assay, this Example describesa method for detecting telomerase activity in a single cell. Singlecells can be obtained by various means, such as by serial dilution orusing a fluorescence activated cell sorter (FACS) sorting either wholecell lines or specifically marked populations of cells. The lattermethod is illustrated in the present Example. The cells are marked withfluorescently labelled or labelable antibodies, which antibodiesrecognize a specific marker. The marker can differentiate cells ofdifferent life spans, function or are differentially expressed.

Cells were sorted into 25 μl of preparatory buffer containing 20 mMTris-HCl (pH 8.3), 1.5 mM MgCl₂, 63 mM KCl, 1 mM EGTA, 1 mg/mL BSA, 0.5%Tween 20, 50 mM dNTPs, 100 ng of TS oligonucleotide, and DEPC-treatedwater. The buffer was placed in 8-tube microtiter format PCR strips. Theconcentration of Tween 20 was sufficient to lyse the cell membrane. Thereaction time used in this Example, although not limiting, was 60minutes at 30° C. The incubation was performed in the block of amicrotiter format Perkin Elmer 9600 thermal cycler. One can also use aheat block or water bath.

Following incubation, an additional 25 μl of amplification buffer wasadded to each reaction tube. The amplification buffer contained the sameingredients noted above except the TS oligonucleotide was replaced by100 ng of gamma end-labelled return primer, ACX. The ACX oligonucleotidewas labelled in a reaction containing T4 polynucleotide kinase (NEB),10×PNK buffer (NEB), and a ratio of 100 μCi of 3000 Ci/mmol γ-³² P ATPper 1 μg of ACX. T4 kinase was used at a ratio of 40 U per 1 μg of ACXand incubated at 37° C. for 30 minutes, followed by a heat treatment of65° C. for 15 minutes to inactivate the kinase. Taq DNA polymerase (2 U;Boehringer Mannheim) was added to the amplification buffer andamplification was performed in a Perkin Elmer 9600 thermal cycler for 32cycles of 94° C., 30 seconds and 60° C., 30 seconds. Products wereanalyzed by electrophoresis in 0.6×TBE on 15% polyacrylamidenon-denaturing gels. Those of skill in the art will recognize that theratio of radioactive label to primer allows for the preparation of aprimer with a high specific activity resulting in a strong signal fromamplified products and detection of telomerase activity at the level ofa single cell.

EXAMPLE 12 Method of Detecting Telomerase Activity from Body Fluids

This Example provides a non-invasive, simple method, particularly usefulin a clinical setting, for collecting cells from body fluids for use intelomerase activity assays. For illustrative purposes, the method isdescribed for collecting cells from the urogenitary tract; however, itshould be noted that the method is not limited to use with urine, butcan be applied to other body fluids, such as, saliva, phlegm, sputum,blood, fine needle aspirates of tumors (e.g., breast tumors, prostatetumors, or other tumor types where fine needle aspirates are used).Furthermore, it will be apparent to one of ordinary skill in the artthat numerous other variations of the methods are possible.

(A) Sample preparation and storage

Method 1

1. Collect voided urine (30-40 ml) in a 50 ml centrifuge tube.

2. Centrifuge at 1000 g for 15 minutes.

3. Carefully discard supernatant so that the pellet is not disturbed.

4. Resuspend pellet in 30 ml of PBS; repellet by centrifugation.

5. Resuspend pellet in 1 ml of PBS, transfer to a 1.5 ml centrifuge tubeand repellet by centrifugation.

6. Establish cell count by using a Coulter counter or hemocytometer.

7. Carefully discard all supernatant.

One can freeze the cell pellet for shipping on dry ice or storage at-80° C. at this point, if desired.

Method 2

1. Collect voided urine (30-40 ml) in 50 ml centrifuge tube.

2. Add 100% glycerol to the collected urine to a final concentration of20%, or add 100% DMSO to the collected urine to a final concentration of10%.

One can keep the treated sample on dry ice for shipping or store at -80°C. at this point, if desired. Before use, the sample is treated asdescribed in steps 2 to 7 of Method 1.

Method 3

1. Collect voided urine and establish cell count by using a Coultercounter or hemocytometer.

2. Filter voided urine (30≧40 ml) through a 0.45 micron filter.

3. Pass 10 ml of PBS through the same filter.

One can seal the filter in a sterile plastic bag, and ship on dry ice orstore at -80° C. at this point, if desired.

(B) Extraction Procedures

Extraction procedures for pelleted cells.

1. Add 20 μl of CHAPS lysis buffer to 1×10⁶ cells or less. If the cellnumber is not known, add a volume of lysis buffer equal to thepacked-cell volume.

2. Follow the standard CHAPS extraction method described in Example 1 toobtain an extract.

Extraction Procedure for cells collected on a filter

1. Cut the filter into small pieces (˜2 mm square).

2. Resuspend the filter pieces in CHAPS lysis buffer (20 μl of CHAPSlysis buffer for 1×10⁶ cells), making sure that the volume of lysisbuffer is equal to or greater than the packed volume of the filterpieces.

3. Follow the standard CHAPS extraction method described in Example 1 toobtain an extract.

(C) TRAP analysis of the urine-derived extract

Extracts (2-5 μl) are used in a standard TRAP assay with 30-35 PCRcycles as described in Example 2. Sensitivity can be increased byaddition of one or more radioactively-labelled dNTPs, in addition to theend-labelled primers. The presence of telomerase activity is correlatedwith the presence of cancer cells in the urine sample and a diagnosticfor urogenitary cancer.

As described above, the method can be used for any body fluid or fineneedle aspirate, thus allowing the presence of telomerase activity to becorrelated with the presence of cancer cells in the fluid or aspirateand a diagnostic for the particular cancer, e.g., lung cancer whensputum or phlegm is the tested fluid, and breast cancer when a fineneedle aspirate of breast or other (e.g., prostate) tissue is tested.

EXAMPLE 13 TRAP Assay Reagents and Kit Formats

In this Example, a variety of reagents and kit formats are provided forthe practitioner's convenience in carrying out the TRAP assay. In partA, a CHAPS lysis buffer is described. In part B, a TRAP internal controlis described. In part C, various kit formats are described. It will beapparent that variation in the reagents and kits are possible dependingon their intended use.

(A) CHAPS Lysis Buffer

A preferred CHAPS lysis buffer has the composition: 10 mM Tris-Cl, pH7.5; 1 mM MgCl₂ ; 1 mM EGTA; 0.1 mM benzamidine; 5 mM β-mercaptoethanol;0.5% CHAPS; 10% glycerol. Addition of KCl to a concentration of 1 mM,and an increase in the concentration of CHAPS detergent to 3%, in theCHAPS lysis buffer, increases the efficiency of the telomeraseextraction 2-5 fold. Thus, a modified CHAPS lysis buffer for use in theTRAP assay contains 10 mM Tris-Cl, pH 7.5; 1 mM MgCl₂ ; 1 mM EGTA; 0.1mM 4-(2-aminoethyl)-benzenesulfonylfluoride (AEBSF) or benzamidine; 5 mMβ-mercaptoethanol; 0.5-3% CHAPS; and 1 mM Cl.

B TRAP internal control (TSNT)

The internal control TSNT, having the sequence5'-AATCCGTCGAGCAGAGTTAAAAGGCCGAGAAGCGAT-3' (SEQ ID NO:5), can beamplified by the TS telomerase substrate primer and a return primer, NT,having the sequence 5'-ATCGCTTCTCGGCCTTTT-3' (SEQ ID NO:6). The NT isnot a substrate for telomerase. This control can be incorporated into aTRAP assay kit, optionally included in the 10×TRAP buffer (at aconcentration of ˜0.002 amol/μl) or in the primer mixture (0.01amol/μl), and results in a TRAP product of 36 bp. The above primer pairsand internal control are merely illustrative; any primer pair andcomplementary control can be substituted therefor.

(C) TRAP Kit Formats

A wide variety of kits and components can be prepared according to thepresent invention, depending upon the intended user of the kit and theparticular needs of the user. Illustrative kits for performing the TRAPassay are provided below. Such kits can be prepared from readilyavailable materials and reagents and can be easily varied as is apparentto one of ordinary skill in the art.

In its simplest form, a kit comprises a telomerase substrate with orwithout instructions. In a further embodiment, a kit comprises atelomerase substrate and a return primer. In another embodiment, a kitcomprises a telomerase substrate, a return primer and one or morebuffers. The buffer can be, for example, a cell lysis buffer,end-labelling buffer or TRAP reaction buffer. The TRAP reaction buffercan optionally contain a control reagent, e.g., control oligonucleotidessuch as TSNT or TSR8, although such control reagents can be providedseparately within the kit. The kit can further comprise positive cellextracts or cell pellets, negative cell extracts or pellets, reactionvessels, water, nucleotides, labels, or enzymes. The positive cellpellet can be 293 cells, HeLa cells or any other telomerase positivecell pellet or a panel of multiple cell types with varying amounts oftelomerase activity. The kits can be provided with or withoutinstructions. Preferably, instructions describe how to use the reagentsin the assay method described in Example 4.

A preferred kit comprises the following reagents:

1. CHAPS lysis buffer (10 mM Tris-Cl, pH 7.5; 1 mM MgCl₂ ; 1 mM EGTA;

0.1 mM Benzamidine; 5 mM β-mercaptoethanol; 0.5% CHAPS; 10% glycerol)

2. 10×TRAP reaction buffer (200 mM Tris-Cl, pH 8.3; 15 mM MgCl₂ ; 630 mMKCl; 0.5% Tween 20; 10 mM EGTA; 1 mg/ml BSA)

3. 50×dNTP mix (2.5 mM dATP, 2.5 mM dGTP, 2.5 mM dCTP, and 2.5 mM dTTP)

4. TS primer (0.1 μl)

5. Water (PCR grade; protease, DNase and RNase-free)

6. Positive control cell pellet (10⁶ cells) or a panel of multiple celltypes with varying amount of telomerase activity.

It will be apparent to one of ordinary skill in the art that aparticular reagent concentration can be varied without detrimentaleffect, and further such variation in a stock solution may or may notreflect variation in the concentration of the reagent when in use.

A particularly preferred kit format further comprises a TRAP primer mix(e.g., ACX 0.1 μg/l; NT 0.1 μg/μl; TSNT 0.01 amol/μl) optionally with aquantitation standard (e.g., TSR8; 0.1 amol/μl).

In another embodiment the kit comprises CHAPS lysis buffer, 10×TRAPreaction buffer containing TSNT (0.002 amol/μl), 50×dNTP mix, TS primer(1 μg/μl), water (PCR grade; protease, DNase and RNase-free), a positivecontrol cell pellet (10⁶ cells) or a panel of multiple cell types withvarying amount of telomerase activity, TRAP reaction tubes (0.1 μg ACTsealed with wax), Taq DNA polymerase (5 U/μl), optionally provided with10×End-labelling buffer (100 mM Tris-OAc; 100 mM MgOAc; 500 mM KOAc),polynucleotide kinase (1 U/μl) and gel loading dye. Alternatively, theTRAP reaction tubes described above can be replaced with ACX primer(50×concentration, 0.1 μg/μl).

EXAMPLE 14 Telomerase Activity Detection by Branched DNA (bDNA) Probes

This Example illustrates the use of bDNA probes for detecting telomeraseactivity in a microtiter plate format. The use of bDNA probes in themethods of the invention are not limited to such a format, as the bDNAprobes can be used in various ways, for example, in in situ detection oftelomerase extension products. For the convenience of the practitioner,it should be noted that reagents for bDNA are available from ChironCorp., CA., and oligonucleotides are available from Synthetic GeneticsCorp., CA. Alternatively, nucleic acids can be linked to a solid surfaceusing conventional attachment chemistry techniques, for example, viaamide or ester linkages.

In one format, multi-well plates are prepared with the telomerASEsubstrate oligonucleotide, TS, (5'-AATCCGTCGAGCAGAGTT-3'; SEQ ID NO:3)bound to the plate at its 5' end. Cell extracts are prepared asdescribed in Example 1. Telomerase buffer (100 μl; 20 mM Tris-Cl pH 8.3,1.5 mM MgCl₂, 63 mM KCl, 0.05% Tween 20, 1 mM EGTA, 0.1 mg/ml BSA, 50 μMdNTPs) and 5 μl of CHAPS telomerase cell extract are added to theTS-bound microtiter plates and incubated for 30 minutes to 2 hours at30° C. The reaction mix is then removed from the well and the wellwashed twice with 200 μl of 1×SSC (8.76 g/l NaCl, 4.41 g/l Na citrate,pH7) at room temperature. Fifty microliters of 1×SSC containing ˜15 pmolof bDNA probe specific for the telomeric repeats (i.e., containing atleast three repeats of 5'-(CCCTAA)-3'; SEQ ID NO:17) is then added tothe well and incubated at ˜55° C. for 30 minutes with gentle shaking.The bDNA probe mix is then removed from the well and the well washedtwice with 200 μl of 0.1×SSC at 37° C. Fifty microliters of 1×SSCcontaining ˜50 pmol of a secondary probe (e.g., an FITC-labelled 18-meroligonucleotide) specific for the branched arms of the bDNA is thenadded to the well (U.S. Pat. No.: 5,124,246. Urdea, 1994) and incubatedat ˜55° C. for 30 minutes with gentle shaking. The solution is removedfrom the well and the well washed twice with 0.1×SSC at 37° C. beforeadding 200 μl of 0.1×SSC. Telomerase products are then detected by anappropriate means, for example, by employing a fluorescent plate readerwhen a fluorescent label is used.

A further illustrative format involves the immobilization of thetelomerase substrate to a microtiter plate using complementary nucleicacids. Telomerase buffer (100 μl; 20 mM Tris-Cl pH 8.3, 1.5 mM MgCl₂, 63mM KCl, 0.05% Tween 20, 1 mM EGTA, 0.1 mg/ml BSA, 50 μM dNTPs;)containing 15 pmol of TS primer is added to a sterile standardmicrotiter plate together with 5 μl of CHAPS telomerase cell extract(the amount of extract can be as high as 50% of the total reactionvolume). The plate is incubated for 30 minutes to 2 hours at 30° C.,after which the solution is transferred to a second microtiter platehaving complementary TS primers bound by their 5' ends (e.g., one ormore repeats of 5'-AACTCTGCTCGACGGATT; SEQ ID NO:24). The second plateis then incubated at ˜55° C. for 30 minutes with gentle shaking beforeremoving the solution from the well and washing the well twice with 200μl of 1×SSC at 37° C. Fifty microliters of 1×SSC containing ˜15 pmol ofbDNA probe specific for the telomeric repeats is then added to the well.The plate is incubated at ˜55° C. for 30 minutes with gentle shakingafter which the solution is removed from the well. The well is thenwashed twice with 200 μl of 0.1×SSC at 37° C. Fifty microliters of 1×SSCcontaining ˜50 pmol of rhodamine-labelled secondary probe specific forthe branched arms of the bDNA is then added to the well. Afterincubating the plate at ˜55° C. for 30 minutes with gentle shaking, thesolution is removed and the well is then washed twice with 0.1×SSC at37° C. The fluorescence can be conveniently detected using a fluorescentplate reader after addition of 200 μl of 0.1×SSC although other methodsexist, such as direct visualization.

Various modifications of these formats are possible, such as, performingthe telomerase reaction described above in a complementary TS-boundmicrotiter plate, thus eliminating the transfer step, immobilizing afterthe telomerase extension reaction with nucleic acids complementary totelomerase repeats or immobilizing prior to the telomerase reactionusing nucleic acids complementary to the telomerase substrate.Furthermore, a wide variety of labels can be used other than afluorescent label and the signal from such labels can be increased byprobing the bDNA specific for the telomerase extension product with asecond bDNA probe specific for the first bDNA branches, in which casethe second bDNA probe is labelled (directly or indirectly with a furtherprobe).

All publications and patent applications mentioned in this specificationare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference. The inventionnow being fully described, it will be apparent to one of ordinary skillin the art that many changes and modifications can be made theretowithout departing from the spirit or scope of the appended claims.

    __________________________________________________________________________    SEQUENCE LISTING    (1) GENERAL INFORMATION:    (iii) NUMBER OF SEQUENCES: 27    (2) INFORMATION FOR SEQ ID NO:1:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:    CCCTTACCCTTACCCTTACCCTAA24    (2) INFORMATION FOR SEQ ID NO:2:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:    GCGCGGCTAACCCTAACCCTAACC24    (2) INFORMATION FOR SEQ ID NO:3:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 18 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:    AATCCGTCGAGCAGAGTT18    (2) INFORMATION FOR SEQ ID NO:4:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 30 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:    GCGCGGCTTACCCTTACCCTTACCCTAACC30    (2) INFORMATION FOR SEQ ID NO:5:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 36 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:    AATCCGTCGAGCAGAGTTAAAAGGCCGAGAAGCGAT36    (2) INFORMATION FOR SEQ ID NO:6:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 18 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:    ATCGCTTCTCGGCCTTTT18    (2) INFORMATION FOR SEQ ID NO:7:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 21 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:    AACCCTAACCCTAACTCTGCT21    (2) INFORMATION FOR SEQ ID NO:8:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 23 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: synthetic    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:    CCTAACCCTAACCCCACTATGCT23    (2) INFORMATION FOR SEQ ID NO:9:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:    CCTAACCCTAACCCTGTATATGCT24    (2) INFORMATION FOR SEQ ID NO:10:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 33 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:    GCGCGGCTTACCCTTACCCTTACCCTAACCAAT33    (2) INFORMATION FOR SEQ ID NO:11:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 23 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:    CCCAATCCGTCGAGCAGAGTTAG23    (2) INFORMATION FOR SEQ ID NO:12:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 22 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:    TAACTCTGCTCGACGGATTCCC22    (2) INFORMATION FOR SEQ ID NO:13:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 21 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:    GGGTAACCCTAACCCTAACCC21    (2) INFORMATION FOR SEQ ID NO:14:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 19 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14:    GGTTAGGGTTAGGGTTAAA19    (2) INFORMATION FOR SEQ ID NO:15:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 18 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15:    GTTAGGGTTAGGGTTAGG18    (2) INFORMATION FOR SEQ ID NO:16:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 18 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: synthetic    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16:    TTAGGGTTAGGGTTAGGG18    (2) INFORMATION FOR SEQ ID NO:17:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 18 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17:    CCCTAACCCTAACCCTAA18    (2) INFORMATION FOR SEQ ID NO:18:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18:    CCCTAACCCTAACCCTAACCCTAA24    (2) INFORMATION FOR SEQ ID NO:19:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 62 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19:    AATCCGTCGAGCAGAGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG62    (2) INFORMATION FOR SEQ ID NO:20:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 30 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20:    CCCTAACCCTAACCCTAACCCTAACCCTAA30    (2) INFORMATION FOR SEQ ID NO:21:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 18 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21:    TTTCCCTTTCCCTTTCCC18    (2) INFORMATION FOR SEQ ID NO:22:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22:    TTTCCCTTTCCCTTTCCCTTTCCC24    (2) INFORMATION FOR SEQ ID NO:23:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:23:    CTTACCCTTACCCTTACCCTAACC24    (2) INFORMATION FOR SEQ ID NO:24:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 18 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24:    AACTCTGCTCGACGGATT18    (2) INFORMATION FOR SEQ ID NO:25:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:25:    GCCCAATCCGTCGAGCAGAGTTAG24    (2) INFORMATION FOR SEQ ID NO:26:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 24 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26:    CTAACTCTGCTCGACGGATTGGGC24    (2) INFORMATION FOR SEQ ID NO:27:    (i) SEQUENCE CHARACTERISTICS:    (A) LENGTH: 33 base pairs    (B) TYPE: nucleic acid    (C) STRANDEDNESS: single    (D) TOPOLOGY: linear    (ii) MOLECULE TYPE: DNA (synthetic)    (iii) HYPOTHETICAL: NO    (iv) ANTI-SENSE: NO    (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27:    CTCGGTACCAAGCTTCTAACCCTAACCCTAACC33    __________________________________________________________________________

What is claimed is:
 1. A method for determining whether a cell samplecontains telomerase activity, said method comprising the steps of:(a)collecting a cell sample; (b) incubating said cell sample in a reactionmixture comprising an exogenous telomerase substrate under conditionssuch that telomerase can catalyze extension of said telomerase substrateby addition of telomeric repeat sequences; (c) replicating said extendedtelomerase substrate; and (d) correlating presence of telomeraseactivity in said cell sample with presence of said extended telomerasesubstrate and absence of telomerase activity in said cell sample withabsence of said extended telomerase substrate.
 2. The method of claim 1,wherein said telomerase substrate lacks a telomeric repeat sequence andsaid replicating step comprises adding to said reaction mixture atemplate-dependent DNA polymerase and a primer that will hybridize tosaid extended telomerase substrate and be extended by said DNApolymerase to form a complementary copy of said extended telomerasesubstrate if an extended telomerase substrate is present in saidreaction mixture.
 3. The method of claim 2, wherein said replicatingstep further comprises the steps of:(1) heating said reaction mixture todenature duplex DNA molecules; and (2) cooling said reaction mixture toa temperature at which complementary nucleic acids can hybridize andsaid primer can extend if extended telomerase substrates are present. 4.The method of claim 3, wherein said heating and cooling steps arerepeated at least 5 times, and said primer is present in amountssufficient for the formation of extended primers during each coolingstep.
 5. The method of claim 3, wherein said DNA polymerase is athermostable template-dependent DNA polymerase and said primer isextended by addition of nucleotides to said primer by said DNApolymerase.
 6. The method of claim 2, wherein said telomerase substratelacking a telomeric repeat sequence is 5'-AATCCGTCGAGCAGAGTT-3' (SEQ IDNO:3).
 7. The method of claim 2, wherein said reaction mixture comprisesa labelled telomerase substrate or a labelled primer.
 8. The method ofclaim 7, wherein said primer comprises a fluorescent label and aquenching dye and further comprises non-complementary sequences at the3'-end of said primer.
 9. The method of claim 2, wherein said primercomprises a non-telomeric repeat sequence at a 5'-end of said primer.10. The method of claim 2, wherein said primer is5'-CCCTTACCCTTACCCTTACCCTAA-3' (SEQ ID NO: 1),5'-GCGCGGCTAACCCTAACCCTAACC-3' (SEQ ID NO:2) or5'-GCGCGGCTTACCCTTACCCTTACCCTAACC-3' (SEQ ID NO:4).
 11. The method ofclaim 2, further comprising adding to said reaction mixture anoligonucleotide that will hybridize to said extended telomerasesubstrate, or said complementary copy at a site 3' to said primer, saidoligonucleotide comprising a fluorescent label and a quenching dye. 12.The method of claim 2, wherein said replicating step further comprisesadding to said reaction mixture an oligonucleotide control for primerextension.
 13. The method of claim 2, wherein the presence of extendedtelomerase substrate is detected by incorporating a label into saidcomplementary copy of said extended telomerase substrate, said labelselected from the group consisting of a radioactive label, a fluorescentlabel, a phosphorescent label, a chromogen, an enzyme, an enzymesubstrate, biotin, avidin and digoxigenin.
 14. The method of claim 2,wherein the presence of extended telomerase substrate is detected usinga branched DNA probe.
 15. The method of claim 1, wherein saidreplicating step comprises adding to said reaction mixture athermostable template-dependent DNA ligase, an oligonucleotide ligomerthat will hybridize to said extended telomerase substrate, and a primerthat will hybridize to said extended telomerase substrate and beextended by ligation of said oligonucleotide ligomer to said primer bysaid DNA ligase if an extended telomerase substrate is present in saidcell sample.
 16. The method of claim 1, wherein said cell sample is ahuman cell sample.
 17. A method for determining whether a cell samplecontains telomerase activity, said method comprising the steps of:(a)incubating a cell sample or a cell extract in a reaction mixturecomprising a telomerase substrate and a buffer in which telomerase cancatalyze extension of said telomerase substrate by addition of telomericrepeat sequences; (b) adding to said reaction mixture atemplate-dependent RNA polymerase that recognizes a promoter sequenceoperably linked to said telomerase substrate; (c) allowing said RNApolymerase to form an RNA copy of said extended telomerase substrate ifan extended telomerase substrate is present in said reaction mixture;and (d) correlating presence of telomerase activity in said cell samplewith presence of RNA copies of said extended telomerase substrate andabsence of telomerase activity in said cell sample with absence of saidRNA copies.
 18. The method of claim 17, further comprising adding tosaid reaction mixture a template-dependent DNA polymerase and a primersufficiently complementary to a telomeric repeat to hybridizespecifically thereto and said primer is extended by addition ofnucleotides to said primer by said DNA polymerase.
 19. The method ofclaim 18, wherein said primer comprises at least one telomeric repeatsequence.
 20. The method of claim 17, wherein said RNA polymeraserecognizes a single-stranded nucleic acid substrate.
 21. The method ofclaim 20, wherein said RNA polymerase is an N4 RNA polymerase.
 22. Themethod of claim 17, wherein said RNA polymerase is selected from thegroup consisting of an SP6 RNA polymerase, a T7 RNA polymerase and a T3RNA polymerase.
 23. The method of claim 17, wherein said cell extract isprepared by lysing cells in said cell sample in a buffer comprising anon-ionic or zwitterionic detergent.
 24. A method for determiningwhether a cell sample contains telomerase activity, said methodcomprising the steps of:(a) incubating a cell sample or a cell extractin a reaction mixture comprising a telomerase substrate lacking atelomeric repeat sequence and a buffer in which telomerase can catalyzeextension of said telomerase substrate by addition of telomeric repeatsequences; (b) immobilizing said telomerase substrate; (c) adding tosaid reaction mixture a probe comprising a sequence sufficientlycomplementary to the extended telomerase substrate to hybridizespecifically thereto under conditions such that if an extendedtelomerase substrate is present in said reaction mixture, said probewill hybridize to said extended telomerase substrate; and (d)correlating presence of telomerase activity in said cell sample withpresence of said probe hybridized to extended telomerase substrate andabsence of telomerase activity in said cell sample with absence ofhybridization of said probe.
 25. The method of claim 24, wherein saidcell extract is prepared by lysing cells in said cell sample in a buffercomprising a non-ionic or zwitterionic detergent.
 26. The method ofclaim 24, wherein said probe is a branched DNA probe.
 27. The method ofclaim 24, wherein said probe is a labelled probe.
 28. The method ofclaim 24, wherein said hybridized probe is detected using a nucleic aciddye.
 29. The method of claim 24, wherein said probe comprises a sequencecomplementary to a telomeric repeat sequence.
 30. The method of claim24, wherein said probe is a biotinylated probe and said probe isdetected by tyramide signal amplification.
 31. The method of claim 24,wherein said telomerase substrate is immobilized after said incubatingstep with said cell extract. substrate.
 32. The method of claim 31,wherein telomeric repeat sequences added to said telomerase substrateduring said incubating step are immobilized and said probe comprises asequence complementary to said telomerase substrate.
 33. The method ofclaim 31, wherein said probe is complementary to said telomeric repeatsequences.
 34. A kit for detecting telomerase activity, said kitcomprising:(a) a telomerase substrate; and (b) a primer comprising asequence complementary to a telomeric repeat sequence.
 35. The kit ofclaim 34 wherein said kit further comprises a cell lysis buffer and anassay buffer.
 36. The kit of claim 34, wherein said kit furthercomprises an oligonucleotide control for primer extension and a cellpellet.
 37. The kit of claim 34, wherein said kit further comprises anoligonucleotide control for primer extension, and a cell sample or acell extract.
 38. The kit of claim 34, wherein said primer is selectedfrom the group consisting of 5'-CCCTTACCCTTACCCTTACCCTAA-3'(SEQ ID NO:1), 5'-GCGCG GCTAACCCTAACCCTAACC-3' (SEQ ID NO:2) and5'-GCGCGGCTTACCCTTA CCCTTACCCTAACC-3'(SEQ ID NO:4).
 39. The kit of claim34, wherein said telomerase substrate is 5'-AATCCGTCGAGCAGAGTT-3' (SEQID NO:3), said primer is 5'-GCGCGGCTTA CCCTTACCCTTACCCTAACC-3' (SEQ IDNO:4) and said kit further comprises a CHAPS lysis buffer, 10×TRAPreaction buffer, a stock solution of dATP, dGTP, CHAPS lysis buffer,10×TRAP reaction buffer, a stock solution of dATP, dGTP, dCTP and dTTP,5'-AATCCGTCGAGCAGAGTTAAAAGGCCGAGAAGCGAT-3' (SEQ ID NO:5),5'-TAACATCGCTTCTCGGCCTTT-3' (SEQ ID NO:6),5'-AATCCGTCGAGCAGAGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG-3'(SEQ ID NO: 19), water and a positive control cell pellet.40. A purified preparation of an oligonucleotide wherein saidoligonucleotide is 5'-AATCC GTCGAGCAGAGTTAAAAGGCCGAGAAGCGAT-3' (SEQ IDNO:5) or 5'-TAAC ATCGCTTCTCGGCCTTTT-3' (SEQ ID NO:6).
 41. The kit ofclaim 34, wherein said telomerase substrate lacks a telomeric repeatsequence.
 42. A method for determining whether a cell sample containstelomerase activity, said method comprising the steps of:(a) collectinga cell sample or a cell extract; (b) incubating said cell sample or saidcell extract in a reaction mixture comprising a telomerase substrateunder conditions such that telomerase can catalyze extension of saidtelomerase substrate by addition of telomeric repeat sequences; (c)amplifying said extended telomerase substrate, wherein said amplifyingis mediated by a template-dependent ligase, a template-dependent RNApolymerase or a branched nucleic acid probe; and (d) correlatingpresence of telomerase activity in said cell sample with presence ofsaid extended telomerase substrate and absence of telomerase activity insaid cell sample with absence of said extended telomerase substrate. 43.The method of claim 42, wherein said telomerase substrate lacks atelomeric repeat sequence.
 44. The method of claim 42, wherein saidamplifying step further comprises adding to said reaction mixture atemplate-dependent DNA polymerase and a primer that will hybridize tosaid extended telomerase substrate and be extended by said DNApolymerase to form a complementary copy of said extended telomerasesubstrate if an extended telomerase substrate is present in saidreaction mixture.